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Donnellan SC, Catullo RA, Rowley JJL, Doughty P, Price L, Hines HB, Richards SJ. Revision of Litoria rothii (Anura: Pelodryadidae) from northern Australia. Zootaxa 2023; 5352:73-108. [PMID: 38221459 DOI: 10.11646/zootaxa.5352.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Indexed: 01/16/2024]
Abstract
Litoria rothii is a widespread pelodryadid frog with a charismatic laughing advertisement call, distributed across the Australian Monsoon Tropics and southern New Guinea. Given its large distribution spanning well-known biogeographic barriers, variation in male advertisement calls and the prevalence of unresolved species complexes in the Australian frog fauna, we examine the genetic, morphological and acoustic diversity in the species from across its range. Our analyses reveal the presence of a previously unrecognised species in western parts of the range of L. rothii sensu lato, which we describe herein as a new species. Litoria ridibunda sp. nov. is distinguished from L. rothii on the basis of paraphyly of nuclear gene trees with L. everetti from Indonesia, colour patterns on the posterior thigh and male advertisement calls. Compared to L. rothii, the new species has a less contrasting pattern on the posterior thigh and a male advertisement call with a greater number of notes per call and a greater call duration. In particular, the magnitude of call differences between the species is highest where the ranges of the two species are in proximity in north-western Queensland. Our study further emphasises the undiagnosed diversity that remains in Australian frogs, even in relatively large, charismatic, frequently encountered species that often share human dwellings.
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Affiliation(s)
- S C Donnellan
- South Australian Museum; North Terrace; Adelaide; SA; 5000; Australia.
| | - R A Catullo
- School of Biological Sciences; University of Western Australia; Nedlands; WA; 6009; Australia.
| | - J J L Rowley
- Australian Museum Research Institute; Australian Museum; 1 William St; Sydney; NSW; 2010; Australia; Centre for Ecosystem Science; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney; NSW; 2052; Australia.
| | - P Doughty
- Collections & Research; Western Australian Museum; 49 Kew St; Welshpool; WA; 6106 Australia.
| | - L Price
- School of Biological Sciences; The University of Adelaide; Adelaide; SA; 5005 Australia.
| | - H B Hines
- Queensland Parks and Wildlife Service and Partnerships; Department of Environment and Science; PO Box 64; Bellbowrie; Qld; 4070; Australia; Honorary Research Fellow; Biodiversity; Queensland Museum; PO Box 3300; South Brisbane; Qld; 4101; Australia.
| | - S J Richards
- South Australian Museum; North Terrace; Adelaide; SA; 5000; Australia; Museum and Art Gallery of the Northern Territory; GPO Box 4646; Darwin; NT; 0801; Australia.
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KSH, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity. eLife 2020; 9:e62765. [PMID: 33350381 PMCID: PMC7775107 DOI: 10.7554/elife.62765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
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Affiliation(s)
- Chyi Yin Gwee
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Kritika M Garg
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Balaji Chattopadhyay
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Keren R Sadanandan
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Tri Haryoko
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Malcolm CK Soh
- University of Western Australia, School of Biological SciencesPerthAustralia
| | - Kelvin S-H Peh
- University of Southampton, School of Biological Sciences, UniversitySouthamptonUnited Kingdom
| | - Karen MC Rowe
- Sciences Department, Museums VictoriaMelbourneAustralia
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah KualaDarussalamIndonesia
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal UniversityXuzhouChina
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
- Center for Tropical Veterinary Studies – One Health Collaboration Center, Universitas Syiah KualaDarussalamIndonesia
| | - Guinevere OU Wogan
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeleyUnited States
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Frank E Rheindt
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
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Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird. Heredity (Edinb) 2019; 123:608-621. [PMID: 30874632 PMCID: PMC6972870 DOI: 10.1038/s41437-019-0206-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 11/09/2022] Open
Abstract
Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.
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Norman JA, Christidis L, Schodde R. Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0364-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Marki PZ, Fjeldså J, Irestedt M, Jønsson KA. Molecular phylogenetics and species limits in a cryptically coloured radiation of Australo-Papuan passerine birds (Pachycephalidae: Colluricincla). Mol Phylogenet Evol 2018. [PMID: 29526804 DOI: 10.1016/j.ympev.2018.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds. In line with previous studies, we find that one species, the little shrikethrush (C. megarhyncha) is characterized by deep divergences among populations. Delimitation results suggest that these clades represent distinct species and we consequently propose a new classification. Furthermore, our findings suggest that C. megarhyncha melanorhyncha of Biak Island does not belong in this genus, but is nested within the whistlers (Pachycephala) as sister to P. phaionota. This study represents a useful example of species delimitation when phenotypic variation is limited or poorly defined.
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Affiliation(s)
- Petter Z Marki
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318 Oslo, Norway.
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Knud A Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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Calderón L, Campagna L, Wilke T, Lormee H, Eraud C, Dunn JC, Rocha G, Zehtindjiev P, Bakaloudis DE, Metzger B, Cecere JG, Marx M, Quillfeldt P. Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove. BMC Evol Biol 2016; 16:237. [PMID: 27821052 PMCID: PMC5100323 DOI: 10.1186/s12862-016-0817-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. RESULTS Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. CONCLUSIONS We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.
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Affiliation(s)
- Luciano Calderón
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany.
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
| | - Hervé Lormee
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Villiers en Bois, Chizé, 79360, France
| | - Cyril Eraud
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Villiers en Bois, Chizé, 79360, France
| | - Jenny C Dunn
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln, LN6 7TS, UK
| | - Gregorio Rocha
- Department of Agro-forestry Engineering, University of Extremadura, Avda. Virgen del Puerto 2, Plasencia, Cáceres, 10600, Spain
| | - Pavel Zehtindjiev
- Bulgarian Academy of Sciences, Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, Sofia, 1113, Bulgaria
| | - Dimitrios E Bakaloudis
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, PO Box 241, Thessaloniki, 541 24, Greece
| | | | - Jacopo G Cecere
- Instituto Superiore per la Protezione e la Ricerca Ambientale, Via Ca' Fornacetta 9, Ozzano Dell'Emilia, (BO), 40064, Italy
| | - Melanie Marx
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
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Sardell JM, Uy JAC. Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species ofMyzomelahoneyeaters. Evolution 2016; 70:257-69. [DOI: 10.1111/evo.12864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/22/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Jason M. Sardell
- Department of Biology; University of Miami; Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of Biology; University of Miami; Coral Gables Florida 33146
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Mohd-Azlan J, Noske RA, Lawes MJ. Resource Partitioning by Mangrove Bird Communities in North Australia. Biotropica 2014. [DOI: 10.1111/btp.12108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jayasilan Mohd-Azlan
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin Northern Territory 0909 Australia
- Department of Zoology; Faculty of Resource Science and Technology; Universiti Malaysia Sarawak; Kota Samarahan Sarawak 94300 Malaysia
| | - Richard A. Noske
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin Northern Territory 0909 Australia
| | - Michael J. Lawes
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin Northern Territory 0909 Australia
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Georges A, Zhang X, Unmack P, Reid BN, Le M, McCord WP. Contemporary genetic structure of an endemic freshwater turtle reflects Miocene orogenesis of New Guinea. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12176] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arthur Georges
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Xiuwen Zhang
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Peter Unmack
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Brenden N. Reid
- Department of Forest and Wildlife Ecology; University of Wisconsin; 1630 Linden Drive Madison WI 53706 USA
| | - Minh Le
- Faculty of Environmental Sciences; Hanoi University of Science; 334 Nguyen Trai Road Hanoi Vietnam
- Centre for Natural Resources and Environmental Studies; 19 Le Thanh Tong Street Hanoi Vietnam
- Department of Herpetology; American Museum of Natural History; New York NY 10024 USA
| | - William P. McCord
- East Fishkill Animal Hospital; 455, Route 82 Hopewell Junction NY 12533 USA
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Andersen MJ, Nyári ÁS, Mason I, Joseph L, Dumbacher JP, Filardi CE, Moyle RG. Molecular systematics of the world's most polytypic bird: thePachycephala pectoralis/melanura(Aves: Pachycephalidae) species complex. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12088] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Michael J. Andersen
- Department of Ecology and Evolutionary Biology and Biodiversity Institute; University of Kansas; Lawrence KS 66045 USA
| | - Árpád S. Nyári
- Department of Zoology; Oklahoma State University; 501 Life Sciences West Stillwater OK 74078 USA
| | - Ian Mason
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra ACT 2601 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra ACT 2601 Australia
| | - John P. Dumbacher
- California Academy of Sciences; 55 Music Concourse Drive San Francisco CA 94118 USA
| | - Christopher E. Filardi
- Center for Biodiversity and Conservation; American Museum of Natural History; New York NY 10024 USA
| | - Robert G. Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute; University of Kansas; Lawrence KS 66045 USA
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