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Peacock J, Spellman GM, Field DJ, Mason MJ, Mayr G. Comparative morphology of the avian bony columella. Anat Rec (Hoboken) 2024; 307:1735-1763. [PMID: 37365751 DOI: 10.1002/ar.25278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
In birds, the columella is the only bony element of the sound conducting apparatus, conveying vibrations of the cartilaginous extracolumella to the fluid of the inner ear. Although avian columellar morphology has attracted some attention over the past century, it nonetheless remains poorly described in the literature. The few existing studies mostly focus on morphological descriptions in relatively few taxa, with no taxonomically broad surveys yet published. Here we use observations of columellae from 401 extant bird species to provide a comprehensive survey of columellar morphology in a phylogenetic context. We describe the columellae of several taxa for the first time and identify derived morphologies characterizing higher-level clades based on current phylogenies. In particular, we identify a derived columellar morphology diagnosing a major subclade of Accipitridae. Within Suliformes, we find that Fregatidae, Sulidae, and Phalacrocoracidae share a derived morphology that is absent in Anhingidae, suggesting a secondary reversal. Phylogenetically informed comparisons allow recognition of instances of homoplasy, including the distinctive bulbous columellae in suboscine passerines and taxa belonging to Eucavitaves, and bulging footplates that appear to have evolved at least twice independently in Strigiformes. We consider phylogenetic and functional factors influencing avian columellar morphology, finding that aquatic birds possess small footplates relative to columellar length, possibly related to hearing function in aquatic habitats. By contrast, the functional significance of the distinctive bulbous basal ends of the columellae of certain arboreal landbird taxa remains elusive.
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Affiliation(s)
- John Peacock
- Department of Physiology and Biophysics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature and Science, Denver, Colorado, USA
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
| | - Matthew J Mason
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
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2
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Demmel Ferreira MM, Degrange FJ, Tirao GA. Brain surface morphology and ecological and macroevolutionary inferences of avian New World suboscines (Aves, Passeriformes, Tyrannides). J Comp Neurol 2024; 532:e25617. [PMID: 38629472 DOI: 10.1002/cne.25617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
The New World suboscines (Passeriformes and Tyrannides) are one of the biggest endemic vertebrate radiations in South America, including the families Furnariidae and Tyrannidae. Avian brain morphology is a reliable proxy to study their evolution. The aim of this work is to elucidate whether the brains of these families reflect the ecological differences (e.g., feeding behavior) and to clarify macroevolutionary aspects of their neuroanatomy. Our hypotheses are as follows: Brain size is similar between both families and with other Passeriformes; brain morphology in Tyrannides is the result of the pressure of ecological factors; and brain disparity is low since they share ecological traits. Skulls of Furnariidae and Tyrannidae were micro-computed tomography-scanned, and three-dimensional models of the endocast were generated. Regression analyses were performed between brain volume and body mass. Linear and surface measurements were used to build phylomorphospaces and to calculate the amount of phylogenetic signal. Tyrannidae showed a larger brain disparity than Furnariidae, although it is not shaped by phylogeny in the Tyrannides. Furnariidae present enlarged Wulsts (eminentiae sagittales) but smaller optic lobes, while in Tyrannidae, it is the opposite. This could indicate that in Tyrannides there is a trade-off between the size of these two visual-related brain structures.
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Affiliation(s)
- María Manuela Demmel Ferreira
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Federico Javier Degrange
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Germán Alfredo Tirao
- Instituto de Física Enrique Gaviola (IFEG), Facultad de Matemática, Astronomía y Física (FaMAF), Universidad Nacional de Córdoba (UNC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
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3
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Smith NA, Koeller KL, Clarke JA, Ksepka DT, Mitchell JS, Nabavizadeh A, Ridgley RC, Witmer LM. Convergent evolution in dippers (Aves, Cinclidae): The only wing-propelled diving songbirds. Anat Rec (Hoboken) 2021; 305:1563-1591. [PMID: 34813153 PMCID: PMC9298897 DOI: 10.1002/ar.24820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/19/2022]
Abstract
Of the more than 6,000 members of the most speciose avian clade, Passeriformes (perching birds), only the five species of dippers (Cinclidae, Cinclus) use their wings to swim underwater. Among nonpasserine wing‐propelled divers (alcids, diving petrels, penguins, and plotopterids), convergent evolution of morphological characteristics related to this highly derived method of locomotion have been well‐documented, suggesting that the demands of this behavior exert strong selective pressure. However, despite their unique anatomical attributes, dippers have been the focus of comparatively few studies and potential convergence between dippers and nonpasseriform wing‐propelled divers has not been previously examined. In this study, a suite of characteristics that are shared among many wing‐propelled diving birds were identified and the distribution of those characteristics across representatives of all clades of extant and extinct wing‐propelled divers were evaluated to assess convergence. Putatively convergent characteristics were drawn from a relatively wide range of sources including osteology, myology, endocranial anatomy, integument, and ethology. Comparisons reveal that whereas nonpasseriform wing‐propelled divers do in fact share some anatomical characteristics putatively associated with the biomechanics of underwater “flight”, dippers have evolved this highly derived method of locomotion without converging on the majority of concomitant changes observed in other taxa. Changes in the flight musculature and feathers, reduction of the keratin bounded external nares and an increase in subcutaneous fat are shared with other wing‐propelled diving birds, but endocranial anatomy shows no significant shifts and osteological modifications are limited. Muscular and integumentary novelties may precede skeletal and neuroendocranial morphology in the acquisition of this novel locomotory mode, with implications for understanding potential biases in the fossil record of other such transitions. Thus, dippers represent an example of a highly derived and complex behavioral convergence that is not fully associated with the anatomical changes observed in other wing‐propelled divers, perhaps owing to the relative recency of their divergence from nondiving passeriforms.
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Affiliation(s)
- N Adam Smith
- Campbell Geology Museum, Clemson University, Clemson, South Carolina, USA.,Department of Science and Education, Field Museum of Natural History, Chicago, Illinois, USA
| | - Krista L Koeller
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Julia A Clarke
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | | | - Jonathan S Mitchell
- Department of Biology, West Virginia University Institute of Technology, Beckley, West Virginia, USA
| | - Ali Nabavizadeh
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Ryan C Ridgley
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, USA
| | - Lawrence M Witmer
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, USA
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4
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Rose EM, Prior NH, Ball GF. The singing question: re-conceptualizing birdsong. Biol Rev Camb Philos Soc 2021; 97:326-342. [PMID: 34609054 DOI: 10.1111/brv.12800] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/31/2023]
Abstract
Birdsong has been the subject of broad research from a variety of sub-disciplines and has taught us much about the evolution, function, and mechanisms driving animal communication and cognition. Typically, birdsong refers to the specialized vocalizations produced by oscines. Historically, much of the research on birdsong was conducted in north temperate regions (specifically in Europe and North America) leading to multiple biases. Due to these historic biases these vocalizations are generally considered to be highly sexually dimorphic, heavily shaped by sexual selection and essential for courtship and territoriality. Song is also typically defined as a learned trait shaped by cultural evolution. Together, this framework focuses research specifically on males, particularly during the north temperate breeding season - reflecting and thereby reinforcing this framework. The physiological underpinnings of song often emphasize the role of the hypothalamic-pituitary-gonadal axis (associated with breeding changes) and the song control system (underlying vocal learning). Over the years there has been great debate over which features of song are essential to the definition of birdsong, which features apply broadly to contexts outside males in the north temperate region, and over the importance of having a definition at all. Importantly, the definitions we use can both guide and limit the progress of research. Here, we describe the history of these definitions, and how these definitions have directed and restricted research to focus on male song in sexually selected contexts. Additionally, we highlight the gaps in our scientific knowledge, especially with respect to the function and physiological mechanisms underlying song in females and in winter, as well as in non-seasonally breeding species. Furthermore, we highlight the problems with using complexity and learning as dichotomous variables to categorize songs and calls. Across species, no one characteristic of song - sexual dimorphism, seasonality, complexity, sexual selection, learning - consistently delineates song from other songbird vocal communication. We provide recommendations for next steps to build an inclusive information framework that will allow researchers to explore nuances in animal communication and promote comparative research. Specifically, we recommend that researchers should operationalize the axis of variation most relevant to their study/species by identifying their specific question and the variable(s) of focus (e.g. seasonality). Researchers should also identify the axis (axes) of variation (e.g. degree of control by testosterone) most relevant to their study and use language consistent with the question and axis (axes) of variation (e.g. control by testosterone in the seasonal vocal production of birds).
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Affiliation(s)
- Evangeline M Rose
- Department of Psychology, University of Maryland, College Park, 4094 Campus Dr., College Park, MD, 20742, U.S.A.,Program in Neuroscience and Cognitive Science, University of Maryland, College Park, 0219 Cole Student Activities Building, 4090 Union Drive, College Park, MD, 20742, U.S.A
| | - Nora H Prior
- Department of Psychology, University of Maryland, College Park, 4094 Campus Dr., College Park, MD, 20742, U.S.A.,Program in Neuroscience and Cognitive Science, University of Maryland, College Park, 0219 Cole Student Activities Building, 4090 Union Drive, College Park, MD, 20742, U.S.A
| | - Gregory F Ball
- Department of Psychology, University of Maryland, College Park, 4094 Campus Dr., College Park, MD, 20742, U.S.A.,Program in Neuroscience and Cognitive Science, University of Maryland, College Park, 0219 Cole Student Activities Building, 4090 Union Drive, College Park, MD, 20742, U.S.A
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5
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Xie L, Li M, Duan Y. Analysis of complete mitochondrial genome sequence of bar-tailed Treecreeper certhia himalayana (psittaciformes: Certhiidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:578-580. [PMID: 33628936 PMCID: PMC7889127 DOI: 10.1080/23802359.2021.1875909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Bar-tailed Treecreeper Certhia himalayana usually lives in coniferous or mixed broadleaf-conifer forests, often crawling along the trunk. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of C. himalayana. The whole genome of C. himalayana was 16,852 bp in length, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 25.1% for A, 29.2% for T, 14.5% for C, 31.2% for G, with a GC content of 45.7%. A phylogenetic tree strongly supported that C. himalayana closely related with Family Troglodytidae by highly probability.
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Affiliation(s)
- Li Xie
- School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Ming Li
- Sichuan Kelun Pharmaceutical Research Institute, Chengdu, China
| | - Yubao Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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6
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Ericson PGP, Irestedt M, Nylander JAA, Christidis L, Joseph L, Qu Y. Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics. Syst Biol 2021; 69:820-829. [PMID: 32415976 PMCID: PMC7440736 DOI: 10.1093/sysbio/syaa040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.]
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Les Christidis
- School of Environment, Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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7
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Can't see the “hood” for the trees: Can avian cooperative breeding currently be understood using the phylogenetic comparative method? ADVANCES IN THE STUDY OF BEHAVIOR 2020. [DOI: 10.1016/bs.asb.2019.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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9
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Jønsson KA, Blom MP, Marki PZ, Joseph L, Sangster G, Ericson PG, Irestedt M. Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return. Mol Phylogenet Evol 2019; 137:200-209. [DOI: 10.1016/j.ympev.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/05/2019] [Accepted: 03/22/2019] [Indexed: 12/01/2022]
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10
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Medina I. The role of the environment in the evolution of nest shape in Australian passerines. Sci Rep 2019; 9:5560. [PMID: 30944374 PMCID: PMC6447541 DOI: 10.1038/s41598-019-41948-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/21/2019] [Indexed: 11/30/2022] Open
Abstract
Avian nests present great variation in structure but, after excluding cavity nesters, probably the most obvious difference is that between open and domed nests. Some species lay their eggs in open structures, exposed to environmental variables, while other species build domed, enclosed nests with a roof, which are suggested to protect eggs and nestlings from weather conditions, high radiation levels, and predation. To date it is unclear which variables drove the evolution of different nest types. In this study, environmental and nest type information was extracted for continental Australian passerines, showing that species with open and closed nests are distributed in similar climates. However, species with open nests have larger ranges and are distributed in a wider variety of climatic conditions, suggesting open nests could be an evolutionary key innovation. This analysis was complemented with a detailed study of the evolution of particular nest traits in the largest Australasian avian radiation (Meliphagoidea), confirming that adult body size - but not environment - is an important factor in nest architecture, and larger species tend to build nests that are shallow and supported from underneath. Nest structure is a multidimensional trait that has probably evolved to match the phenotype of the nest owner, but that could also constrain or facilitate establishment in different environments.
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Affiliation(s)
- Iliana Medina
- School of BioSciences, University of Melbourne, Parkville, 3010, VIC, Australia.
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11
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Abstract
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
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Dinh TD, Ngatia JN, Cui LY, Ma Y, Dhamer TD, Xu YC. Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Sci Int Genet 2019; 40:85-95. [PMID: 30780122 DOI: 10.1016/j.fsigen.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023]
Abstract
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.
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Affiliation(s)
- Thi Dao Dinh
- College of Wildlife Resources, Northeast Forestry University, China
| | | | - Liang Yu Cui
- College of Wildlife Resources, Northeast Forestry University, China
| | - Yue Ma
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China
| | | | - Yan Chun Xu
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China; State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, China.
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13
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Ksepka DT, Grande L, Mayr G. Oldest Finch-Beaked Birds Reveal Parallel Ecological Radiations in the Earliest Evolution of Passerines. Curr Biol 2019; 29:657-663.e1. [PMID: 30744971 DOI: 10.1016/j.cub.2018.12.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 11/27/2022]
Abstract
Beak shape plays a key role in avian radiations and is one of the most intensely studied aspects of avian evolution and ecology [1-4]. Perhaps no other group is more closely associated with the study of beak shape than Passeriformes (passerines or perching birds), the most species-rich ordinal clade of modern birds. However, despite their extraordinary present-day diversity, our understanding of early passerine evolution has been hindered by their sparse fossil record [5, 6]. Here, we describe two new species of early Eocene stem passerines from the Green River Formation of the United States and the Messel Formation of Germany. These species are the oldest fossil birds to exhibit a finch-like beak and provide the earliest evidence for a diet focused on small, hard seeds in crown birds. Given that granivory is a key adaptation that allows passerines to exploit open temperate environments, it is notable that both species occurred in subtropical environments [7, 8]. Phylogenetic analyses place both species within the Psittacopedidae, an extinct Eocene clade of zygodactyl stem passeriforms that also includes the slender-beaked nectarivorous Pumiliornis, the short-beaked Psittacopes, and the thrush-beaked Morsoravis. Our results reveal that stem passerines attained a diversity of beak shapes paralleling many of the morphotypes present in extant passerine finches, thrushes, and sunbirds, more than 35 million years before these morphotypes arose in the crown group. Extinction of these ecologically diverse fossil taxa may be linked to more sophisticated nest construction in anisodactyl crown passerines versus cavity-nesting in Eocene zygodactyl stem passerines [9].
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Affiliation(s)
- Daniel T Ksepka
- Bruce Museum, Greenwich, CT 06830, USA; Field Museum of Natural History, Chicago, IL 60605, USA; American Museum of Natural History, New York, NY 10024, USA; Smithsonian Institution, Washington, DC 20013, USA.
| | - Lance Grande
- Field Museum of Natural History, Chicago, IL 60605, USA; American Museum of Natural History, New York, NY 10024, USA; University of Chicago, Chicago, IL 60637, USA
| | - Gerald Mayr
- Senckenberg Research Institute, Frankfurt am Main, Germany
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14
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Crouch NMA, Ramanauskas K, Igić B. Tip-dating and the origin of Telluraves. Mol Phylogenet Evol 2018; 131:55-63. [PMID: 30385308 DOI: 10.1016/j.ympev.2018.10.006] [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: 12/19/2017] [Revised: 09/05/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022]
Abstract
Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves-a clade of birds defined by their arboreality-is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate. Specifically, we use a large collection of morphological character data from arboreal bird fossils, along with combined molecular sequence and morphological character data from extant taxa. Our analyses recover a Late Cretaceous origin for crown Telluraves, with a few lineages crossing the K-Pg boundary. Following the K-Pg boundary, our results show the group underwent rapid diversification, likely benefiting from increased ecological opportunities in the aftermath of the extinction event. We find very little confidence for the precise topological placement of many extinct taxa, possibly due to rapid diversification, paucity of character data, and rapid morphological differentiation during the early history of the group.
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Affiliation(s)
- Nicholas M A Crouch
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Karolis Ramanauskas
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Boris Igić
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
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15
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Smith NA, DeBee AM, Clarke JA. Systematics and phylogeny of the Zygodactylidae (Aves, Neognathae) with description of a new species from the early Eocene of Wyoming, USA. PeerJ 2018; 6:e4950. [PMID: 29967716 PMCID: PMC6022727 DOI: 10.7717/peerj.4950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
Zygodactylidae are an extinct lineage of perching birds characterized by distinct morphologies of the foot and wing elements. Although the clade has a complex taxonomic history, current hypotheses place Zygodactylidae as the sister taxon to Passeriformes (i.e., songbirds). Given the rather sparse fossil record of early passeriforms, the description of zygodactylid taxa is important for inferring potentially ancestral states in the largest radiation of living birds (i.e., the ∼6,000 species of extant passeriforms). Despite the exceptional preservation of many specimens and considerable species diversity in Zygodactylidae, the relationships among species have not been previously evaluated in a phylogenetic context. Herein, we review the fossil record of Zygodactylidae from North America and describe five new well-preserved fossils from the early Eocene Green River Formation of Wyoming. Two specimens are identified as representing a new species and the first records of the taxon Zygodactylus outside Europe. Anatomical comparisons with previously named taxa and the results of phylogenetic analysis including newly described specimens and previously named zygodactylid taxa provide the first hypothesis of the species-level relationships among zygodactylids. The monophyly of Zygodactylidae is supported in these new analyses. However, the monophyly of Primozygodactylus and the taxonomic distinction between Zygodactylus and Eozygodactylus remain unresolved and would likely benefit from the description of additional specimens.
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Affiliation(s)
- N. Adam Smith
- Campbell Geology Museum, Clemson University, Clemson, SC, USA
| | - Aj M. DeBee
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Julia A. Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
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16
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The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes. Genes Genomics 2018; 40:151-165. [PMID: 29892923 DOI: 10.1007/s13258-017-0617-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772 bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.
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17
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Abstract
Studies reconstructing morphological evolution have long relied on simple representations of organismal form or on limited sampling of species, hindering a comprehensive understanding of the factors shaping biological diversity. Here, we combine high-resolution 3D quantification of skull shape with dense taxonomic sampling across a major vertebrate clade, birds, to demonstrate that the avian skull is formed of multiple semi-independent regions that epitomize mosaic evolution, with cranial regions and major lineages evolving with distinct rates and modes. We further show that the evolvability of different cranial regions reflects their disparate embryonic origins. Finally, we present a hypothetical reconstruction of the ancestral bird skull using this high-resolution shape data to generate a detailed estimate of extinct forms in the absence of well-preserved three-dimensional fossils. Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families. We find that the avian cranium is highly modular, consisting of seven independently evolving anatomical regions. The face and cranial vault evolve faster than other regions, showing several bursts of rapid evolution. Other modules evolve more slowly following an early burst. Both the evolutionary rate and disparity of skull modules are associated with their developmental origin, with regions derived from the anterior mandibular-stream cranial neural crest or from multiple embryonic cell populations evolving most quickly and into a greater variety of forms. Strong integration of traits is also associated with low evolutionary rate and low disparity. Individual clades are characterized by disparate evolutionary rates among cranial regions. For example, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close relatives, Falconiformes, exhibit rapid evolution in only the rostrum. Our dense sampling of cranial shape variation demonstrates that the bird skull has evolved in a mosaic fashion reflecting the developmental origins of cranial regions, with a semi-independent tempo and mode of evolution across phenotypic modules facilitating this hyperdiverse evolutionary radiation.
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18
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Suh A, Bachg S, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J. De-novo emergence of SINE retroposons during the early evolution of passerine birds. Mob DNA 2017; 8:21. [PMID: 29255493 PMCID: PMC5729268 DOI: 10.1186/s13100-017-0104-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. RESULTS Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. CONCLUSIONS We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Department of Evolutionary Biology (EBC), Uppsala University, SE-75236 Uppsala, Sweden
| | - Sandra Bachg
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
| | - Stephen Donnellan
- South Australian Museum, Adelaide, SA 5000 Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005 Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601 Australia
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Brandenburg Medical School (MHB), D-16816 Neuruppin, Germany
| | - Jan Ole Kriegs
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- LWL-Museum für Naturkunde, Westfälisches Landesmuseum mit Planetarium, D-48161 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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19
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Barker FK. Molecular Phylogenetics of the Wrens and Allies (Passeriformes: Certhioidea), with Comments on the Relationships ofFerminia. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3887.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- F. Keith Barker
- Department of Ecology, Evolution and Behavior and Bell Museum of Natural History, University of Minnesota
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20
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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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21
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Quispe R, Protazio JMB, Gahr M. Seasonal singing of a songbird living near the equator correlates with minimal changes in day length. Sci Rep 2017; 7:9140. [PMID: 28831057 PMCID: PMC5567256 DOI: 10.1038/s41598-017-08800-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/19/2017] [Indexed: 11/13/2022] Open
Abstract
Behaving in accordance with natural cycles is essential for survival. Birds in the temperate regions use the changes of day length to time their behavior. However, at equatorial latitudes the photoperiod remains almost constant throughout the year, and it is unclear which cues songbirds use to regulate behaviors, such as singing. Here, we investigated the timing of dawn-song of male silver-beaked tanagers in the equatorial lowland Amazonas over two years. In this region, birds experience around nine minutes of annual day length variation, with sunrise times varying by 32 minutes over the year. We show that the seasonal timing of dawn-song was highly regular between years, and was strongly correlated with slight increases in day length. During the singing season the daily dawn-song onset was precisely aligned to variations in twilight time. Thus, although photoperiodic changes near the equator are minimal, songbirds can use day length variation to time singing.
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Affiliation(s)
- Rene Quispe
- Department of Behavioural Neurobiology Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany. .,Departamento Biología Marina, Facultad Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| | - João Marcelo Brazão Protazio
- Department of Behavioural Neurobiology Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany.,Faculdade de Estatística, Universidade Federal do Pará, Rua Augusto Corrêa 01 - Guamá, 66075-110, Belém, PA, Brazil
| | - Manfred Gahr
- Department of Behavioural Neurobiology Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany
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22
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Price JJ, Griffith SC. Open cup nests evolved from roofed nests in the early passerines. Proc Biol Sci 2017; 284:20162708. [PMID: 28148749 PMCID: PMC5310614 DOI: 10.1098/rspb.2016.2708] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/06/2017] [Indexed: 11/12/2022] Open
Abstract
The architectural diversity of nests in the passerine birds (order Passeriformes) is thought to have played an important role in the adaptive radiation of this group, which now comprises more than half of avian species and occupies nearly all terrestrial ecosystems. Here, we present an extensive survey and ancestral state reconstruction of nest design across the passerines, focusing on early Australian lineages and including members of nearly all passerine families worldwide. Most passerines build open cup-shaped nests, whereas a minority build more elaborate domed structures with roofs. We provide strong evidence that, despite their relative rarity today, domed nests were constructed by the common ancestor of all modern passerines. Open cup nests evolved from enclosed domes at least four times independently during early passerine evolution, at least three of which occurred on the Australian continent, yielding several primarily cup-nesting clades that are now widespread and numerically dominant among passerines. Our results show that the ubiquitous and relatively simple cup-shaped nests of many birds today evolved multiple times convergently, suggesting adaptive benefits over earlier roofed designs.
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Affiliation(s)
- J Jordan Price
- Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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23
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MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion. Immunogenetics 2016; 69:101-111. [PMID: 27717988 DOI: 10.1007/s00251-016-0953-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022]
Abstract
The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.
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24
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Moyle RG, Oliveros CH, Andersen MJ, Hosner PA, Benz BW, Manthey JD, Travers SL, Brown RM, Faircloth BC. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Commun 2016; 7:12709. [PMID: 27575437 PMCID: PMC5013600 DOI: 10.1038/ncomms12709] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/26/2016] [Indexed: 12/03/2022] Open
Abstract
Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.
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Affiliation(s)
- Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Carl H. Oliveros
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Peter A. Hosner
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Brett W. Benz
- Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Joseph D. Manthey
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Scott L. Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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25
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Eo SH, An J. Mitochondrial genome sequence of black paradise flycatcher (Aves: Monarchidae) and its phylogenetic position. Mitochondrial DNA B Resour 2016; 1:454-455. [PMID: 33473517 PMCID: PMC7800213 DOI: 10.1080/23802359.2016.1181996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Soo Hyung Eo
- Department of Forest Resources, Kongju National University, Chungnam, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
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26
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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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27
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Claramunt S, Cracraft J. A new time tree reveals Earth history's imprint on the evolution of modern birds. SCIENCE ADVANCES 2015; 1:e1501005. [PMID: 26824065 PMCID: PMC4730849 DOI: 10.1126/sciadv.1501005] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/02/2015] [Indexed: 05/21/2023]
Abstract
Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.
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28
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Garnett ST, Duursma DE, Ehmke G, Guay PJ, Stewart A, Szabo JK, Weston MA, Bennett S, Crowley GM, Drynan D, Dutson G, Fitzherbert K, Franklin DC. Biological, ecological, conservation and legal information for all species and subspecies of Australian bird. Sci Data 2015; 2:150061. [PMID: 26594379 PMCID: PMC4640137 DOI: 10.1038/sdata.2015.61] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 10/02/2015] [Indexed: 11/16/2022] Open
Abstract
We introduce a dataset of biological, ecological, conservation and legal information for every species and subspecies of Australian bird, 2056 taxa or populations in total. Version 1 contains 230 fields grouped under the following headings: Taxonomy & nomenclature, Phylogeny, Australian population status, Conservation status, Legal status, Distribution, Morphology, Habitat, Food, Behaviour, Breeding, Mobility and Climate metrics. It is envisaged that the dataset will be updated periodically with new data for existing fields and the addition of new fields. The dataset has already had, and will continue to have applications in Australian and international ornithology, especially those that require standard information for a large number of taxa.
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Affiliation(s)
- Stephen T Garnett
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin, NT 0909, Australia
| | - Daisy E Duursma
- Department of Biological Sciences, Macquarie University , North Ryde, NSW 2109, Australia
| | - Glenn Ehmke
- BirdLife Australia , 5/60 Leicester St, Carlton, Vic. 3053, Australia
| | - Patrick-Jean Guay
- Institute for Sustainability and Innovation, Victoria University, Footscray Park Campus , PO Box 14428, Melbourne MC, Vic. 8001, Australia
| | - Alistair Stewart
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin, NT 0909, Australia
| | - Judit K Szabo
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin, NT 0909, Australia ; East Asian-Australasian Flyway Partnership Secretariat , 3F G-Tower, 175 Art center-daero (24-4 Songdo-dong), Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Michael A Weston
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Faculty of Science, Engineering and the Built Environment, Deakin University , 221 Burwood Hwy, Burwood, Vic. 3125, Australia
| | | | - Gabriel M Crowley
- The Cairns Institute, James Cook University , PO Box 6811, Cairns, Qld 4870, Australia
| | - David Drynan
- Australian Bird & Bat Banding Scheme , GPO Box 8, Canberra, ACT 2601, Australia
| | - Guy Dutson
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin, NT 0909, Australia ; School of Life and Environmental Sciences, Deakin University , Waurn Ponds, Vic. 3216, Australia
| | - Kate Fitzherbert
- Bush Heritage Australia , PO Box 329, Flinders Lane, Melbourne, Vic. 8009, Australia
| | - Donald C Franklin
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin, NT 0909, Australia
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29
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Gibb GC, England R, Hartig G, McLenachan PAT, Taylor Smith BL, McComish BJ, Cooper A, Penny D. New Zealand Passerines Help Clarify the Diversification of Major Songbird Lineages during the Oligocene. Genome Biol Evol 2015; 7:2983-95. [PMID: 26475316 PMCID: PMC5635589 DOI: 10.1093/gbe/evv196] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Passerines are the largest avian order, and the 6,000 species comprise more than half of all extant bird species. This successful radiation probably had its origin in the Australasian region, but dating this origin has been difficult due to a scarce fossil record and poor biogeographic assumptions. Many of New Zealand’s endemic passerines fall within the deeper branches of the passerine radiation, and a well resolved phylogeny for the modern New Zealand element in the deeper branches of the oscine lineage will help us understand both oscine and passerine biogeography. To this end we present complete mitochondrial genomes representing all families of New Zealand passerines in a phylogenetic framework of over 100 passerine species. Dating analyses of this robust phylogeny suggest Passeriformes originated in the early Paleocene, with the major lineages of oscines “escaping” from Australasia about 30 Ma, and radiating throughout the world during the Oligocene. This independently derived conclusion is consistent with the passerine fossil record.
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Affiliation(s)
- Gillian C Gibb
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Ryan England
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: Forensic Business Group, Institute of Environmental Science and Research (ESR Ltd.), Mt Albert Science Centre, Auckland, New Zealand
| | - Gerrit Hartig
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: Starlims Germany GmbH An Abbott Company, Witten, Germany
| | | | - Briar L Taylor Smith
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Bennet J McComish
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: School of Physical Sciences, University of Tasmania, Hobart, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Kamiński P, Grochowska E, Mroczkowski S, Jerzak L, Kasprzak M, Koim-Puchowska B, Woźniak A, Ciebiera O, Markulak D. Sex ratio of White Stork Ciconia ciconia in different environments of Poland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13194-13203. [PMID: 25940461 DOI: 10.1007/s11356-015-4250-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/17/2015] [Indexed: 06/04/2023]
Abstract
The aim of this study was to analyze the variation in sex ratio of White Stork Ciconia ciconia chicks from differentiated Poland environments. We took under a consideration the impact of Cd and Pb for establish differences among sex ratio in chicks. We also study multiplex PCR employment for establish gender considerations. We collected blood samples via venipuncture of brachial vein of chicks during 2006-2008 breeding seasons at the Odra meadows (SW-Poland; control), which were compared with those from suburbs (SW-Poland), and from copper smelter (S-Poland; polluted) and from swamps near Baltic Sea. We found differences among sex ratio in White Stork chicks from types of environment. Male participation in sex structure is importantly higher in each type of environment excluded suburban areas. Differences in White Stork sex ratio according to the degree of environmental degradation expressed by Cd and Pb and sex-environment-metal interactions testify about the impact of these metals upon sex ratios in storks. Simultaneously, as a result of multiplex PCR, 18S ribosome gene, which served as internal control of PCR, was amplified in male and female storks. It means that it is possible to use primers designed for chicken in order to replicate this fragment of genome in White Stork. Moreover, the use of Oriental White Stork Ciconia boyciana W- chromosome specific primers makes it possible to determine the sex of C. ciconia chicks. Many factors make sex ratio of White Stork changes in subsequent breeding seasons, which depend significantly on specific environmental parameters that shape individual detailed defense mechanisms.
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Affiliation(s)
- Piotr Kamiński
- Collegium Medicum in Bydgoszcz, Department of Ecology and Environmental Protection, Nicolaus Copernicus University in Toruń, Skłodowska-Curie St. 9, 85-094, Bydgoszcz, Poland,
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31
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Bandelj P, Blagus R, Trilar T, Vengust M, Rataj AV. Influence of phylogeny, migration and type of diet on the presence of intestinal parasites in the faeces of European passerine birds (Passeriformes). WILDLIFE BIOLOGY 2015. [DOI: 10.2981/wlb.00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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dos Santos MDS, Kretschmer R, Silva FAO, Ledesma MA, O'Brien PCM, Ferguson-Smith MA, Del Valle Garnero A, de Oliveira EHC, Gunski RJ. Intrachromosomal rearrangements in two representatives of the genus Saltator (Thraupidae, Passeriformes) and the occurrence of heteromorphic Z chromosomes. Genetica 2015; 143:535-43. [PMID: 26092368 DOI: 10.1007/s10709-015-9851-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
Abstract
Saltator is a genus within family Thraupidae, the second largest family of Passeriformes, with more than 370 species found exclusively in the New World. Despite this, only a few species have had their karyotypes analyzed, most of them only with conventional staining. The diploid number is close to 80, and chromosome morphology is similar to the usual avian karyotype. Recent studies using cross-species chromosome painting have shown that, although the chromosomal morphology and number are similar to many species of birds, Passeriformes exhibit a complex pattern of paracentric and pericentric inversions in the chromosome homologous to GGA1q in two different suborders, Oscines and Suboscines. Hence, considering the importance and species richness of Thraupidae, this study aims to analyze two species of genus Saltator, the golden-billed saltator (S. aurantiirostris) and the green-winged saltator (S. similis) by means of classical cytogenetics and cross-species chromosome painting using Gallus gallus and Leucopternis albicollis probes, and also 5S and 18S rDNA and telomeric sequences. The results show that the karyotypes of these species are similar to other species of Passeriformes. Interestingly, the Z chromosome appears heteromorphic in S. similis, varying in morphology from acrocentric to metacentric. 5S and 18S probes hybridize to one pair of microchromosomes each, and telomeric sequences produce signals only in the terminal regions of chromosomes. FISH results are very similar to the Passeriformes already analyzed by means of molecular cytogenetics (Turdus species and Elaenia spectabilis). However, the paracentric and pericentric inversions observed in Saltator are different from those detected in these species, an observation that helps to explain the probable sequence of rearrangements. As these rearrangements are found in both suborders of Passeriformes (Oscines and Suboscines), we propose that the fission of GGA1 and inversions in GGA1q have occurred very early after the radiation of this order.
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Affiliation(s)
- Michelly da Silva dos Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, Pará, Brazil
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A Paleogene origin for crown passerines and the diversification of the Oscines in the New World. Mol Phylogenet Evol 2015; 88:1-15. [PMID: 25837731 DOI: 10.1016/j.ympev.2015.03.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/25/2015] [Accepted: 03/18/2015] [Indexed: 11/24/2022]
Abstract
In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.
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35
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Jønsson KA, Lessard JP, Ricklefs RE. The evolution of morphological diversity in continental assemblages of passerine birds. Evolution 2015; 69:879-89. [PMID: 25655140 DOI: 10.1111/evo.12622] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/24/2015] [Indexed: 11/30/2022]
Abstract
Understanding geographic variation in the species richness and lineage composition of regional biotas is a long-standing goal in ecology. Why do some evolutionary lineages proliferate while others do not, and how do new colonists fit into an established fauna? Here, we analyze the morphological structure of assemblages of passerine birds in four biogeographic regions to examine the relative influence of colonization history and niche-based processes on continental communities of passerine birds. Using morphological traits related to habitat choice, foraging technique, and movement, we quantify the morphological spaces occupied by different groups of passerine birds. We further quantify morphological overlap between groups by multivariate discriminant analysis and null model analyses of trait dispersion. Finally, we use subclade disparity through time to assess the temporal component of morphological evolution. We find mixed support for the prediction, based on priority, that first colonizers constrain subsequent colonizers. Indeed, our results show that the assembly of continental communities is idiosyncratic with regards to the diversification of new clades and the filling of morphospace.
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Affiliation(s)
- Knud Andreas Jønsson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
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36
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Building the avian tree of life using a large-scale, sparse supermatrix. Mol Phylogenet Evol 2015; 84:53-63. [DOI: 10.1016/j.ympev.2014.12.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 11/20/2022]
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37
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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014; 346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Citation(s) in RCA: 1127] [Impact Index Per Article: 112.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
| | - Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andre J Aberer
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Bo Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Benoit Nabholz
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Claudia C Weber
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jianwen Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Nitish Narula
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ganesh Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Volodymyr Zavidovych
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Bhanu Rekepalli
- Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bent Lindow
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA
| | - David Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Richard E Green
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Frederick H Sheldon
- 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
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maria Paula Cruz Schneider
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil
| | - Francisco Prosdocimi
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - José Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Amhed Missael Vargas Velazquez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bent Petersen
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Ponten
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - An Pas
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Tom Bailey
- Dubai Falcon Hospital, Dubai, United Arab Emirates
| | - Paul Scofield
- Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia
| | - Amy C Driskell
- Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Zijun Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yongli Zeng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenyu Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Binghang Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiong Yinqi
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuemei Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Michael Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA
| | - Jon Fjeldsa
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Warren Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Stephen O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - John McCormack
- Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Dave Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany
| | - David P Mindell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wang Jun
- BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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38
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Andersen MJ, Hosner PA, Filardi CE, Moyle RG. Phylogeny of the monarch flycatchers reveals extensive paraphyly and novel relationships within a major Australo-Pacific radiation. Mol Phylogenet Evol 2014; 83:118-36. [PMID: 25463752 DOI: 10.1016/j.ympev.2014.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/01/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Monarch flycatchers are a major component of Australo-Pacific and Wallacean avifaunas. To date, the family has received incomplete attention by molecular systematists who focused on subclades with minimal character and/or taxon sampling. As a result, Monarchidae taxonomy is still out-of-date, and biogeographic reconstructions have been based on poorly-resolved phylogenies, limiting their interpretation. Here, we produced a comprehensive, molecular phylogeny of the Monarchidae inferred from mitochondrial and nuclear loci using both concatenated and multilocus coalescent frameworks. We sampled 92% of the 99 recognized monarchid biological species and included deeper sampling within several phylogenetic species complexes, including Monarcha castaneiventris, Symposiachrus barbatus, and Terpsiphone rufiventer. Melampitta is identified as sister to the monarch flycatchers, which themselves comprise four major lineages. The first lineage comprises Terpsiphone and allies, the second lineage is Grallina, the third is Arses and Myiagra, and the fourth lineage comprises a diverse assemblage of genera including the "core monarchs" and the most geographically isolated groups like Chasiempis (Hawaii) and Pomarea (eastern Polynesia). Gene tree discordance was evident in Myiagra, which has implications for basal lineages in the genus (e.g., M. azureocapilla, M. hebetior, and M. alecto). Numerous genera within the core monarchs are paraphyletic, including Mayrornis and Pomarea, whereas the validity of others such as Metabolus are questionable. We recognize polytypic taxa as multiple species, including Lamprolia victoriae and Myiagra azureocapilla. In general, the topology of species complexes included short internodes that were not well resolved, owing to their rapid diversification across island archipelagos. Terpsiphone rufiventer comprises multiple lineages, including a heretofore-unappreciated West African lineage, but relationships within these rapid radiations will require extensive genomic sampling for further resolution. This study establishes a new benchmark for Monarchidae systematics and it provides an excellent framework for future work on biogeography and character evolution in a diverse Australo-Papuan radiation.
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Affiliation(s)
- Michael J Andersen
- American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA.
| | - Peter A Hosner
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA; Department of Biology, University of Florida, 512 Bartram Hall, Gainesville, FL 32603, USA
| | - Christopher E Filardi
- American Museum of Natural History, Central Park West at 79th St., 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
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39
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Keith Barker F. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Mol Phylogenet Evol 2014; 79:313-24. [DOI: 10.1016/j.ympev.2014.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/31/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
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40
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Shi D, Luo Y, Du Q, Wang L, Zhou M, Ma J, Li R, Chen T, Shaw C. A novel bradykinin-related dodecapeptide (RVALPPGFTPLR) from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis) exhibiting unusual structural and functional features. Toxins (Basel) 2014; 6:2886-98. [PMID: 25268979 PMCID: PMC4210874 DOI: 10.3390/toxins6102886] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/28/2014] [Accepted: 09/12/2014] [Indexed: 02/05/2023] Open
Abstract
Bradykinin-related peptides (BRPs) are significant components of the defensive skin secretions of many anuran amphibians, and these secretions represent the source of the most diverse spectrum of such peptides so far encountered in nature. Of the many families of bioactive peptides that have been identified from this source, the BRPs uniquely appear to represent homologues of counterparts that have specific distributions and receptor targets within discrete vertebrate taxa, ranging from fishes through mammals. Their broad spectra of actions, including pain and inflammation induction and smooth muscle effects, make these peptides ideal weapons in predator deterrence. Here, we describe a novel 12-mer BRP (RVALPPGFTPLR-RVAL-(L1, T6, L8)-bradykinin) from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis). The C-terminal 9 residues of this BRP (-LPPGFTPLR) exhibit three amino acid substitutions (L/R at Position 1, T/S at Position 6 and L/F at Position 8) when compared to canonical mammalian bradykinin (BK), but are identical to the kinin sequence present within the cloned kininogen-2 from the Chinese soft-shelled turtle (Pelodiscus sinensis) and differ from that encoded by kininogen-2 of the Tibetan ground tit (Pseudopodoces humilis) at just a single site (F/L at Position 8). These data would imply that the novel BRP is an amphibian defensive agent against predation by sympatric turtles and also that the primary structure of the avian BK, ornithokinin (RPPGFTPLR), is not invariant within this taxon. Synthetic RVAL-(L1, T6, L8)-bradykinin was found to be an antagonist of BK-induced rat tail artery smooth muscle relaxation acting via the B2-receptor.
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Affiliation(s)
- Daning Shi
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Yu Luo
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Qiang Du
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Jie Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Renjie Li
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Chris Shaw
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
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41
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Bravo GA, Remsen JV, Brumfield RT. Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae). Evolution 2014; 68:2757-74. [DOI: 10.1111/evo.12506] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 06/26/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Gustavo A. Bravo
- Museum of Natural Science; Louisiana State University; Baton Rouge Louisiana 70803
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana 70803
| | - J. V. Remsen
- Museum of Natural Science; Louisiana State University; Baton Rouge Louisiana 70803
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana 70803
| | - Robb T. Brumfield
- Museum of Natural Science; Louisiana State University; Baton Rouge Louisiana 70803
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana 70803
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42
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Cubo J, Baudin J, Legendre L, Quilhac A, De Buffrénil V. Geometric and metabolic constraints on bone vascular supply in diapsids. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jorge Cubo
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
- CNRS; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
| | - Jéromine Baudin
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
- CNRS; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
| | - Lucas Legendre
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
- CNRS; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
| | - Alexandra Quilhac
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
- CNRS; UMR 7193; Institut des Sciences de la Terre Paris (iSTeP); F-75005 Paris France
| | - Vivian De Buffrénil
- Sorbonne Universités; MNHN Muséum National d'Histoire Naturelle; UMR 7207; Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P); F-75005 Paris France
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43
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Coimbra JP, Collin SP, Hart NS. Topographic specializations in the retinal ganglion cell layer of Australian passerines. J Comp Neurol 2014; 522:3609-28. [DOI: 10.1002/cne.23624] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/03/2014] [Accepted: 05/05/2014] [Indexed: 11/08/2022]
Affiliation(s)
- João Paulo Coimbra
- School of Animal Biology, The University of Western Australia; Crawley Western Australia 6009 Australia
- The Oceans Institute, The University of Western Australia; Crawley Western Australia 6009 Australia
- School of Anatomical Sciences, The University of the Witwatersrand; Parktown 2193 Johannesburg South Africa
| | - Shaun P. Collin
- School of Animal Biology, The University of Western Australia; Crawley Western Australia 6009 Australia
- The Oceans Institute, The University of Western Australia; Crawley Western Australia 6009 Australia
| | - Nathan S. Hart
- School of Animal Biology, The University of Western Australia; Crawley Western Australia 6009 Australia
- The Oceans Institute, The University of Western Australia; Crawley Western Australia 6009 Australia
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Abstract
Our knowledge of the avian tree of life remains uncertain, particularly at deeper levels due to the rapid diversification early in their evolutionary history. They are the most abundant land vertebrate on the planet and have been of great historical interest to systematists. Birds are also economically and ecologically important and as a result are intensively studied, yet despite their importance and interest to humans around 13% of taxa currently on the endangered species list perhaps as a result of human activity. Despite all this no comprehensive phylogeny that includes both extinct and extant species currently exists. Here we present a species-level supertree, constructed using the Matrix Representation with Parsimony method, of Aves containing approximately two thirds of all species from nearly 1000 source phylogenies with a broad taxonomic coverage. The source data for the tree were collected and processed according to a strict protocol to ensure robust and accurate data handling. The resulting tree topology is largely consistent with molecular hypotheses of avian phylogeny. We identify areas that are in broad agreement with current views on avian systematics and also those that require further work. We also highlight the need for leaf-based support measures to enable the identification of rogue taxa in supertrees. This is a first attempt at a supertree of both extinct and extant birds, it is not intended to be utilised in an overhaul of avian systematics or as a basis for taxonomic re-classification but provides a strong basis on which to base further studies on macroevolution, conservation, biodiversity, comparative biology and character evolution, in particular the inclusion of fossils will allow the study of bird evolution and diversification throughout deep time.
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Affiliation(s)
- Katie E Davis
- Department of Biology & Biochemistry, University of Bath, Bath, UK
| | - Roderic D M Page
- Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Vetinary and Life Sciences University of Glasgow, Glasgow, UK
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Ma YG, Huang Y, Lei FM. Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2014; 35:81-91. [PMID: 24668650 DOI: 10.11813/j.issn.0254-5853.2014.2.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.
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Affiliation(s)
- Yong-Gui Ma
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huang
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Fu-Min Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Joseph L, Toon A, Nyári ÁS, Longmore NW, Rowe KMC, Haryoko T, Trueman J, Gardner JL. A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical and ecological complexity of a spectacular avian radiation. ZOOL SCR 2014. [DOI: 10.1111/zsc.12049] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra ACT 2601 Australia
| | - Alicia Toon
- Australian Rivers Institute; Griffith School of Environment; Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
| | - Árpád S. Nyári
- Department of Zoology; Oklahoma State University; 501 Life Sciences West Stillwater OK 74078 USA
| | - N. Wayne Longmore
- Sciences Department; Museum Victoria; GPO Box 666 Melbourne Vic. Australia
| | - Karen M. C. Rowe
- Sciences Department; Museum Victoria; GPO Box 666 Melbourne Vic. Australia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense; Research Center for Biology; Indonesian Institute of Sciences; Jl. Raya Jakarta-Bogor KM. 46 Cibinong Indonesia
| | - John Trueman
- Evolution, Ecology and Genetics; Research School of Biology; The Australian National University; Canberra ACT 0200 Australia
| | - Janet L. Gardner
- School of Biological Sciences; Monash University; Melbourne Vic. 3168 Australia
- Evolution, Ecology and Genetics; Research School of Biology; The Australian National University; Canberra ACT 0200 Australia
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Alström P, Hooper DM, Liu Y, Olsson U, Mohan D, Gelang M, Le Manh H, Zhao J, Lei F, Price TD. Discovery of a relict lineage and monotypic family of passerine birds. Biol Lett 2014; 10:20131067. [PMID: 24598108 DOI: 10.1098/rsbl.2013.1067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the 'bombycillids' (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and Bombycilloidea, although the relationships among these were unresolved. We conclude that the spotted wren-babbler represents a relict basal lineage within Passerida with no close extant relatives, and we support the already used name Elachura formosa and propose the new family name Elachuridae for this single species.
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Affiliation(s)
- Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, , 1 Beichen West Road, Chaoyang District, Beijing 100101, People's Republic of China
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48
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Powell AF, Barker FK, Lanyon SM, Burns KJ, Klicka J, Lovette IJ. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae). Mol Phylogenet Evol 2014; 71:94-112. [DOI: 10.1016/j.ympev.2013.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/16/2022]
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49
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Ericson PGP, Klopfstein S, Irestedt M, Nguyen JMT, Nylander JAA. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol Biol 2014; 14:8. [PMID: 24422673 PMCID: PMC3917694 DOI: 10.1186/1471-2148-14-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% of all living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the late Cretaceous. However, previous molecular dating studies have relied heavily on the geological split between New Zealand and Antarctica, assumed to have occurred 85-82 Mya, for calibrating the molecular clock and might thus be circular in their argument. RESULTS This study provides a time-scale for the evolution of the major clades of passerines using seven nuclear markers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealand split from Antarctica 85-52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretations of the New Zealand-Antarctica vicariance event influence our age estimates. Our results suggest that the diversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration for the New Zealand-Antarctica vicariance event (85-52 Mya) dramatically increases the 95% credibility intervals and leads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genes analyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines, which can be used as secondary calibration points in future molecular studies. CONCLUSIONS Our analysis takes recent paleontological and geological findings into account and provides the best estimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporal framework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, and adds to the growing support for a Cretaceous origin of Passeriformes.
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Affiliation(s)
- Per GP Ericson
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Seraina Klopfstein
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Martin Irestedt
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Jacqueline MT Nguyen
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Johan AA Nylander
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
- BILS – Bioinformatics Infrastructure for Life Sciences, University of Linköping, SE–58183 Linköping, Sweden
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50
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Cibois A, Thibault JC, Bonillo C, Filardi CE, Watling D, Pasquet E. Phylogeny and biogeography of the fruit doves (Aves: Columbidae). Mol Phylogenet Evol 2014; 70:442-53. [DOI: 10.1016/j.ympev.2013.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 11/24/2022]
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