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Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
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2
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García-Navas V, Tobias JA, Schweizer M, Wegmann D, Schodde R, Norman JA, Christidis L. Trophic niche shifts and phenotypic trait evolution are largely decoupled in Australasian parrots. BMC Ecol Evol 2021; 21:212. [PMID: 34837943 PMCID: PMC8626917 DOI: 10.1186/s12862-021-01940-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Trophic shifts from one dietary niche to another have played major roles in reshaping the evolutionary trajectories of a wide range of vertebrate groups, yet their consequences for morphological disparity and species diversity differ among groups. METHODS Here, we use phylogenetic comparative methods to examine whether the evolution of nectarivory and other trophic shifts have driven predictable evolutionary pathways in Australasian psittaculid parrots in terms of ecological traits such as body size, beak shape, and dispersal capacity. RESULTS We found no evidence for an 'early-burst' scenario of lineage or morphological diversification. The best-fitting models indicate that trait evolution in this group is characterized by abrupt phenotypic shifts (evolutionary jumps), with no sign of multiple phenotypic optima correlating with different trophic strategies. Thus, our results point to the existence of weak directional selection and suggest that lineages may be evolving randomly or slowly toward adaptive peaks they have not yet reached. CONCLUSIONS This study adds to a growing body of evidence indicating that the relationship between avian morphology and feeding ecology may be more complex than usually assumed and highlights the importance of adding more flexible models to the macroevolutionary toolbox.
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Affiliation(s)
- Vicente García-Navas
- Department of Integrative Ecology, Doñana Biological Station EBD (CSIC), Seville, Spain.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), University of Lisbon, Lisbon, Portugal.
| | - Joseph A Tobias
- Department of Life Sciences (Silwood Park), Faculty of Natural Sciences, Imperial College London, London, UK
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Richard Schodde
- Australian National Wildlife Collection, CSIRO Sustainable Ecosystems, Canberra, Australia
| | | | - Les Christidis
- Southern Cross University, Coffs Harbour, NSW, Australia
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3
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Grealy A, Langmore NE, Joseph L, Holleley CE. Genetic barcoding of museum eggshell improves data integrity of avian biological collections. Sci Rep 2021; 11:1605. [PMID: 33452280 PMCID: PMC7810714 DOI: 10.1038/s41598-020-79852-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/07/2020] [Indexed: 11/19/2022] Open
Abstract
Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird’s egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen’s appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species’ accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.
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Affiliation(s)
- Alicia Grealy
- Langmore Group, Research School of Biology, Australian National University, Building 46, Canberra, 0200, Australia. .,Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, 2601, Australia.
| | - Naomi E Langmore
- Langmore Group, Research School of Biology, Australian National University, Building 46, Canberra, 0200, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, 2601, Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, 2601, Australia
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4
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No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus). DIVERSITY 2019. [DOI: 10.3390/d11040058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.
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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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6
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Wallis GP, Jorge F. Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia. Mol Ecol 2018; 27:4368-4396. [DOI: 10.1111/mec.14875] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
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7
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De Pietri VL, Scofield RP, Hand SJ, Tennyson AJD, Worthy TH. Sheathbill-like birds (Charadriiformes: Chionoidea) from the Oligocene and Miocene of Australasia. J R Soc N Z 2016. [DOI: 10.1080/03036758.2016.1194297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Phylogenetic analysis of the Australian rosella parrots (Platycercus) reveals discordance among molecules and plumage. Mol Phylogenet Evol 2015; 91:150-9. [DOI: 10.1016/j.ympev.2015.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/25/2022]
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9
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Schweizer M, Wright TF, Peñalba JV, Schirtzinger EE, Joseph L. Molecular phylogenetics suggests a New Guinean origin and frequent episodes of founder-event speciation in the nectarivorous lories and lorikeets (Aves: Psittaciformes). Mol Phylogenet Evol 2015; 90:34-48. [PMID: 25929786 DOI: 10.1016/j.ympev.2015.04.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/01/2015] [Accepted: 04/12/2015] [Indexed: 01/18/2023]
Abstract
The lories and lorikeets (Aves: Loriinae: Loriini) are a readily recognizable, discrete group of nectarivorous parrots confined to the Indo-Pacific region between Wallace's Line and the Pitcairn Island group in the central-east Pacific Ocean. We present the first phylogenetic analysis of all currently recognized genera in the group using two mitochondrial and five nuclear loci. Our analyses suggest a New Guinean origin for the group at about 10million years ago (95% HPD 4.8-14.8) but this origin must be interpreted within the context of that island's complicated, recent geological history. That is, the origin and early diversification of the group may have taken place as New Guinea's Central Cordillera arose and the final constituent terranes that form present-day New Guinea were accreted. The latter activity may have promoted dispersal as a key element in the group's history. We have detected several instances of dispersal out of New Guinea that we argue constitute instances of founder-event speciation. Some phenotypically cohesive genera are affirmed as monophyletic but other genera are clearly in need of taxonomic dismantlement and reclassification. We recognize Parvipsitta Mathews, 1916 for two species usually placed in Glossopsitta and we advocate transfer of Chalcopsitta cardinalis into Pseudeos Peters, 1935. Other non-monophyletic genera such as Charmosyna, Psitteuteles and, probably, Trichoglossus, require improved taxon sampling and further phylogenetic analysis before their systematics can be resolved. Cursory examination of trait mapping across the group suggests that many traits are ancestral and of little use in determining genus-level systematics.
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Affiliation(s)
- Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, CH 3005 Bern, Switzerland.
| | - Timothy F Wright
- Department of Biology, MSC 3AF, New Mexico State University, Las Cruces, NM 88003, USA.
| | - Joshua V Peñalba
- Research School of Biology, Australian National University, Building 116, Acton, Australian Capital Territory 0200, Australia.
| | - Erin E Schirtzinger
- Department of Biology, MSC 3AF, New Mexico State University, Las Cruces, NM 88003, USA.
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Australian Capital Territory 2601, Australia.
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10
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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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11
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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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12
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Diversification in a biodiversity hotspot – The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae). Mol Phylogenet Evol 2013; 68:567-81. [DOI: 10.1016/j.ympev.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 03/28/2013] [Accepted: 04/01/2013] [Indexed: 12/24/2022]
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