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Müller IA, Thörn F, Rajan S, Ericson PGP, Dumbacher JP, Maiah G, Blom MPK, Jønsson KA, Irestedt M. Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae). PLoS One 2024; 19:e0293715. [PMID: 38781204 PMCID: PMC11115331 DOI: 10.1371/journal.pone.0293715] [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: 10/17/2023] [Accepted: 03/26/2024] [Indexed: 05/25/2024] Open
Abstract
The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.
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Affiliation(s)
- Ingo A. Müller
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Filip Thörn
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Samyuktha Rajan
- Department of Zoology, Division of Ethology, Stockholm University, Stockholm, Sweden
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John P. Dumbacher
- Department of Ornithology and Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America
| | - Gibson Maiah
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Mozes P. K. Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Knud A. Jønsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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2
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Roycroft E, Fabre PH, MacDonald AJ, Moritz C, Moussalli A, Rowe KC. New Guinea uplift opens ecological opportunity across a continent. Curr Biol 2022; 32:4215-4224.e3. [PMID: 36057260 DOI: 10.1016/j.cub.2022.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia; Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anna J MacDonald
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Adnan Moussalli
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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3
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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4
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Natusch DJD, Lyons JA. Geographic frequency and ecological correlates of juvenile colour polymorphism in green pythons (Morelia azurea and Morelia viridis). AUST J ZOOL 2020. [DOI: 10.1071/zo21002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Colour polymorphisms are common in nature, but their evolutionary significance and the mechanisms maintaining them sometimes remain poorly understood. Polymorphic green pythons (Morelia azurea and Morelia viridis) are born either red or yellow. Several processes are proposed to maintain such polymorphisms, and the assumption that colour is adaptive predicts that it may be correlated with a series of life-history and/or ecological traits. We examined 1090 green pythons from northern Australia and New Guinea and reveal strong geographic variation in the frequency of juvenile polymorphism. Some variation is explained by known genetic structure among populations, while stochastic processes (e.g. bottlenecks, founder effects) likely explain remaining variation. The yellow juvenile morph occurs in all populations of M. azurea and M. viridis, whereas the red morph occurs only in some populations of M. azurea and at varying frequencies. Yellow and red juveniles did not differ in morph-specific survival, sex ratios, morphology (tail length, head shape and mass) or diet. We discuss our results in relation to several hypotheses relating to maintenance of colour polymorphisms in nature. Although inconclusive, we are reluctant to suggest that colour is non-adaptive, and encourage additional experimental field research on the significance of polymorphism in these taxa.
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Natusch DJ, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Moriarty Lemmon E, Riyanto A, Keogh JS, Donnellan S. Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia. Mol Phylogenet Evol 2020; 142:106640. [DOI: 10.1016/j.ympev.2019.106640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/30/2019] [Accepted: 10/05/2019] [Indexed: 02/01/2023]
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6
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Murray CM, Russo P, Zorrilla A, McMahan CD. Divergent Morphology among Populations of the New Guinea Crocodile, Crocodylus novaeguineae (Schmidt, 1928): Diagnosis of an Independent Lineage and Description of a New Species. COPEIA 2019. [DOI: 10.1643/cg-19-240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Christopher M. Murray
- Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave, Cookeville, Tennessee 38505
| | - Peter Russo
- Louisiana State University Health Sciences Center, School of Allied Health, New Orleans, Louisiana 70112;
| | - Alexander Zorrilla
- Louisiana State University Health Sciences Center, School of Medicine, New Orleans, Louisiana 70112;
| | - Caleb D. McMahan
- Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, Illinois 60605;
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7
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Tallowin OJ, Tamar K, Meiri S, Allison A, Kraus F, Richards SJ, Oliver PM. Early insularity and subsequent mountain uplift were complementary drivers of diversification in a Melanesian lizard radiation (Gekkonidae: Cyrtodactylus). Mol Phylogenet Evol 2018; 125:29-39. [DOI: 10.1016/j.ympev.2018.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 02/20/2018] [Accepted: 03/14/2018] [Indexed: 11/30/2022]
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8
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Lam A, Toussaint EFA, Kindler C, Van Dam MH, Panjaitan R, Roderick GK, Balke M. Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes. Mol Ecol 2018; 27:3541-3554. [PMID: 30030868 DOI: 10.1111/mec.14807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 01/30/2023]
Abstract
Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD DNA sequencing approach to investigate the population structure and phylogeography of a putatively widespread New Guinean species of diving beetle, Philaccolilus ameliae (Dytiscidae). We find that P. ameliae is a complex of morphologically cryptic, but geographically and genetically well-differentiated clades. The pattern of population connectivity is consistent with theoretical predictions associated with stable lotic habitats. However, in two clades, we find a more complex pattern of low population differentiation, revealing dispersal across rugged mountains and watersheds of New Guinea up to 430 km apart. These results, while surprising, were also consistent with the original formulation of the habitat template concept by Southwood, involving lineage-idiosyncratic evolution in response to abiotic factors. In our system, low population differentiation might reflect a young species in a phase of range expansion utilizing vast available habitat. We suggest that predictions of life history variation resulting from the dichotomy between lotic and lentic organisms require more attention to habitat characterization and microhabitat choice. Our results also underpin the necessity to study fine-scale processes but at a larger geographical scale, as compared to solely documenting macroecological patterns, to understand ecological drivers of regional biodiversity. Comprehensive sampling especially of tropical lineages in complex and threatened environments such as New Guinea remains a critical challenge.
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Affiliation(s)
- Athena Lam
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Department of Environmental Science, Policy and Management, University of California, Berkeley, California.,Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | | | | | - Matthew H Van Dam
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Department of Environmental Science, Policy and Management, University of California, Berkeley, California.,Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | - Rawati Panjaitan
- Department of Biology, Faculty of Sciences and Mathematics, State University of Papua (UNIPA), Manokwari, West Papua, Indonesia
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,GeoBioCenter, Ludwig-Maximilians-University, München, Germany
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9
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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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10
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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11
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Jønsson KA, Borregaard MK, Carstensen DW, Hansen LA, Kennedy JD, Machac A, Marki PZ, Fjeldså J, Rahbek C. Biogeography and Biotic Assembly of Indo-Pacific Corvoid Passerine Birds. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022813] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Michael Krabbe Borregaard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Daniel Wisbech Carstensen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Louis A. Hansen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Jonathan D. Kennedy
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Antonin Machac
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Petter Zahl Marki
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
- Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
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12
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Linck EB, Hanna ZR, Sellas A, Dumbacher JP. Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecol Evol 2017; 7:4755-4767. [PMID: 28690805 PMCID: PMC5496524 DOI: 10.1002/ece3.3065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.
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Affiliation(s)
- Ethan B. Linck
- Department of BiologyBurke Museum of Natural History & CultureUniversity of WashingtonSeattleWAUSA
| | - Zachary R. Hanna
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCAUSA
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCAUSA
- Ornithology & MammologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Anna Sellas
- Center for Comparative GenomicsCalifornia Academy of SciencesSan FranciscoCAUSA
| | - John P. Dumbacher
- Ornithology & MammologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Center for Comparative GenomicsCalifornia Academy of SciencesSan FranciscoCAUSA
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13
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Irestedt M, Batalha-Filho H, Ericson PGP, Christidis L, Schodde R. Phylogeny, biogeography and taxonomic consequences in a bird-of-paradise species complex, Lophorina–Ptiloris (Aves: Paradisaeidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Janda M, Matos-Maraví P, Borovanska M, Zima J, Youngerman E, Pierce NE. Phylogeny and population genetic structure of the ant genus Acropyga (Hymenoptera : Formicidae) in Papua New Guinea. INVERTEBR SYST 2016. [DOI: 10.1071/is14050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spatial isolation and geological history are important factors in the diversification and population differentiation of species. Here we describe distributional patterns of ants in the genus Acropyga across Papua New Guinea (PNG), a highly biodiverse but little-studied region. We estimate phylogenetic relationships among currently recognised species of Acropyga and assess population genetic structure of the widespread species, A. acutiventris, across lowland areas of the island. We find that species of Acropyga present in PNG diversified during the Pliocene, between six and two million years ago. Most species now exhibit a patchy distribution that does not show a strong signal of geological history. However, the population genetic structure of the widespread species A. acutiventris has been influenced by geography, habitat association and, possibly, historical habitat fragmentation. There is a significant effect of isolation-by-distance within continuous lowland forest, and proximity to Australia has had a larger impact in structuring populations of A. acutiventris in PNG than has the Central Papuan Cordillera. This study is the first to describe population genetic patterns of an ant species in Papua New Guinea.
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15
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Linck E, Schaack S, Dumbacher JP. Genetic differentiation within a widespread “supertramp” taxon: Molecular phylogenetics of the Louisiade White-eye ( Zosterops griseotinctus ). Mol Phylogenet Evol 2016; 94:113-21. [DOI: 10.1016/j.ympev.2015.08.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/22/2015] [Accepted: 08/20/2015] [Indexed: 11/26/2022]
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16
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Irestedt M, Batalha-Filho H, Roselaar CS, Christidis L, Ericson PGP. Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus). ZOOL SCR 2015. [DOI: 10.1111/zsc.12163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
| | | | - Cees S. Roselaar
- Naturalis Biodiversity Center; Darwinweg 2 PO Box 9517 RA Leiden 2300 The Netherlands
| | - Les Christidis
- National Marine Science Centre; Southern Cross University; Coffs Harbour NSW 2450 Australia
| | - Per G. P. Ericson
- Department of Zoology; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
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17
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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18
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Sangster G, Luksenburg JA. Declining rates of species described per taxonomist: slowdown of progress or a side-effect of improved quality in taxonomy? Syst Biol 2014; 64:144-51. [PMID: 25190593 DOI: 10.1093/sysbio/syu069] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA
| | - Jolanda A Luksenburg
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA
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19
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Geographic and Sexual Variations in Body Size, Morphology, and Diet among Five Populations of Green Pythons (Morelia viridis). J HERPETOL 2014. [DOI: 10.1670/12-207] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Schweizer M, Güntert M, Seehausen O, Leuenberger C, Hertwig ST. Parallel adaptations to nectarivory in parrots, key innovations and the diversification of the Loriinae. Ecol Evol 2014; 4:2867-83. [PMID: 25165525 PMCID: PMC4130445 DOI: 10.1002/ece3.1131] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/12/2022] Open
Abstract
Specialization to nectarivory is associated with radiations within different bird groups, including parrots. One of them, the Australasian lories, were shown to be unexpectedly species rich. Their shift to nectarivory may have created an ecological opportunity promoting species proliferation. Several morphological specializations of the feeding tract to nectarivory have been described for parrots. However, they have never been assessed in a quantitative framework considering phylogenetic nonindependence. Using a phylogenetic comparative approach with broad taxon sampling and 15 continuous characters of the digestive tract, we demonstrate that nectarivorous parrots differ in several traits from the remaining parrots. These trait-changes indicate phenotype-environment correlations and parallel evolution, and may reflect adaptations to feed effectively on nectar. Moreover, the diet shift was associated with significant trait shifts at the base of the radiation of the lories, as shown by an alternative statistical approach. Their diet shift might be considered as an evolutionary key innovation which promoted significant non-adaptive lineage diversification through allopatric partitioning of the same new niche. The lack of increased rates of cladogenesis in other nectarivorous parrots indicates that evolutionary innovations need not be associated one-to-one with diversification events.
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Affiliation(s)
- Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde BernBernastrasse 15, CH 3005, Bern, Switzerland
| | - Marcel Güntert
- Naturhistorisches Museum der Burgergemeinde BernBernastrasse 15, CH 3005, Bern, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Macroevolution, Institute of Ecology & Evolution, University of BernBaltzerstrasse 6, CH 3012, Bern, Switzerland
- Fish Ecology and Evolution, EAWAGSeestrasse 79, CH 6047, Kastanienbaum, Switzerland
| | - Christoph Leuenberger
- Department of Quantitative Economics, University of FribourgBoulevard de Pérolles 90, CH 1700, Fribourg, Switzerland
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde BernBernastrasse 15, CH 3005, Bern, Switzerland
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21
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The towering orogeny of New Guinea as a trigger for arthropod megadiversity. Nat Commun 2014; 5:4001. [DOI: 10.1038/ncomms5001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
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22
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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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23
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Nyári ÁS, Joseph L. Comparative phylogeography of Australo-Papuan mangrove-restricted and mangrove-associated avifaunas. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700; Canberra; ACT; 2601; Australia
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24
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Toussaint EFA, Sagata K, Surbakti S, Hendrich L, Balke M. Australasian sky islands act as a diversity pump facilitating peripheral speciation and complex reversal from narrow endemic to widespread ecological supertramp. Ecol Evol 2013; 3:1031-49. [PMID: 23610642 PMCID: PMC3631412 DOI: 10.1002/ece3.517] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 11/10/2022] Open
Abstract
The Australasian archipelago is biologically extremely diverse as a result of a highly puzzling geological and biological evolution. Unveiling the underlying mechanisms has never been more attainable as molecular phylogenetic and geological methods improve, and has become a research priority considering increasing human-mediated loss of biodiversity. However, studies of finer scaled evolutionary patterns remain rare particularly for megadiverse Melanesian biota. While oceanic islands have received some attention in the region, likewise insular mountain blocks that serve as species pumps remain understudied, even though Australasia, for example, features some of the most spectacular tropical alpine habitats in the World. Here, we sequenced almost 2 kb of mitochondrial DNA from the widespread diving beetle Rhantus suturalis from across Australasia and the Indomalayan Archipelago, including remote New Guinean highlands. Based on expert taxonomy with a multigene phylogenetic backbone study, and combining molecular phylogenetics, phylogeography, divergence time estimation, and historical demography, we recover comparably low geographic signal, but complex phylogenetic relationships and population structure within R. suturalis. Four narrowly endemic New Guinea highland species are subordinated and two populations (New Guinea, New Zealand) seem to constitute cases of ongoing speciation. We reveal repeated colonization of remote mountain chains where haplotypes out of a core clade of very widespread haplotypes syntopically might occur with well-isolated ones. These results are corroborated by a Pleistocene origin approximately 2.4 Ma ago, followed by a sudden demographic expansion 600,000 years ago that may have been initiated through climatic adaptations. This study is a snapshot of the early stages of lineage diversification by peripatric speciation in Australasia, and supports New Guinea sky islands as cradles of evolution, in line with geological evidence suggesting very recent origin of high altitudes in the region.
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A multilocus coalescent analysis of the speciational history of the Australo-Papuan butcherbirds and their allies. Mol Phylogenet Evol 2013; 66:941-52. [DOI: 10.1016/j.ympev.2012.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 11/19/2012] [Accepted: 11/23/2012] [Indexed: 11/16/2022]
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26
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Natusch DJD, Lyons JA. Relationships between ontogenetic changes in prey selection, head shape, sexual maturity, and colour in an Australasian python (Morelia viridis). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01941.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Kearns AM, Joseph L, Omland KE, Cook LG. Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird? Mol Ecol 2011; 20:5042-59. [PMID: 22060632 DOI: 10.1111/j.1365-294x.2011.05330.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea.
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Affiliation(s)
- Anna M Kearns
- School of Biological Sciences, The University of Queensland, Brisbane, Qld 4072, Australia.
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