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Sánchez Reyes LL, McTavish EJ, O’Meara B. DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life. Syst Biol 2024; 73:470-485. [PMID: 38507308 PMCID: PMC11282365 DOI: 10.1093/sysbio/syae015] [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: 06/22/2022] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
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Affiliation(s)
- Luna L Sánchez Reyes
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Emily Jane McTavish
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
| | - Brian O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
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2
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Jiang C, Kang H, Zhou Y, Zhu W, Zhao X, Mohamed N, Li B. Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes). Life (Basel) 2024; 14:881. [PMID: 39063634 PMCID: PMC11278119 DOI: 10.3390/life14070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.
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Affiliation(s)
- Chuan Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Hui Kang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Yang Zhou
- BGI Research, Shenzhen 518083, China;
- BGI Research, Wuhan 430074, China
| | - Wenwen Zhu
- School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Xilong Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Nassoro Mohamed
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Bo Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin 150040, China
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3
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Schlenker P, Coye C, Leroux M, Chemla E. The ABC-D of animal linguistics: are syntax and compositionality for real? Biol Rev Camb Philos Soc 2023; 98:1142-1159. [PMID: 36960599 DOI: 10.1111/brv.12944] [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: 09/12/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/25/2023]
Abstract
In several animal species, an alarm call (e.g. ABC notes in the Japanese tit Parus minor) can be immediately followed by a recruitment call (e.g. D notes) to yield a complex call that triggers a third behaviour, namely mobbing. This has been taken to be an argument for animal syntax and compositionality (i.e. the property by which the meaning of a complex expression depends on the meaning of its parts and the way they are put together). Several additional discoveries were made across species. First, in some cases, animals respond with mobbing to the order alarm-recruitment but not to the order recruitment-alarm. Second, animals sometimes respond similarly to functionally analogous heterospecific calls they have never heard before, and/or to artificial hybrid sequences made of conspecific and heterospecific calls in the same order, thus adding an argument for the productivity of the relevant rules. We consider the details of these arguments for animal syntax and compositionality and argue that, with one important exception (Japanese tit ABC-D sequences), they currently remain ambiguous: there are reasonable alternatives on which each call is a separate utterance and is interpreted as such ('trivial compositionality'). More generally, we propose that future studies should argue for animal syntax and compositionality by explicitly pitting the target theory against two deflationary analyses: the 'only one expression' hypothesis posits that there is no combination in the first place, for example just a simplex ABCD call; while the 'separate utterances' hypothesis posits that there are separate expressions (e.g. ABC and D), but that they form separate utterances and are neither syntactically nor semantically combined.
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Affiliation(s)
- Philippe Schlenker
- Département d'Etudes Cognitives, Ecole Normale Supérieure, Institut Jean-Nicod (ENS - EHESS - CNRS), 29, rue d'Ulm, Paris, 75005, France
- PSL Research University, 60 Rue Mazarine, Paris, 75006, France
- Department of Linguistics, New York University, 10 Washington Place, New York, NY, 10003, USA
| | - Camille Coye
- Département d'Etudes Cognitives, Ecole Normale Supérieure, Institut Jean-Nicod (ENS - EHESS - CNRS), 29, rue d'Ulm, Paris, 75005, France
- PSL Research University, 60 Rue Mazarine, Paris, 75006, France
| | - Maël Leroux
- Department of Comparative Language Science, University of Zürich, Affolternstrasse 56, Zürich, CH-8050, Switzerland
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Affolternstrasse 56, Zürich, CH-8050, Switzerland
| | - Emmanuel Chemla
- PSL Research University, 60 Rue Mazarine, Paris, 75006, France
- LSCP (ENS - EHESS - CNRS), Département d'Etudes Cognitives, Ecole Normale Supérieure, 29, rue d'Ulm, Paris, 75005, France
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4
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Tura V, Kretschmer R, Sassi FDMC, de Moraes RLR, Barcellos SA, de Rosso VO, de Souza MS, Cioffi MDB, Gunski RJ, Garnero ADV. Chromosomal Evolution of Suboscines: Karyotype Diversity and Evolutionary Trends in Ovenbirds (Passeriformes, Furnariidae). Cytogenet Genome Res 2023; 162:644-656. [PMID: 36996794 DOI: 10.1159/000530428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/28/2023] [Indexed: 04/01/2023] Open
Abstract
Furnariidae (ovenbirds) is one of the most diversified families in the Passeriformes order and Suboscines suborder. Despite the great diversity of species, cytogenetic research is still in its early stages, restricting our knowledge of their karyotype evolution. We combined traditional and molecular cytogenetic analyses in three representative species, Synallaxis frontalis, Syndactyla rufosuperciliata, and Cranioleuca obsoleta, to examine the chromosomal structure and evolution of ovenbirds. Our findings revealed that all the species studied had the same diploid number (2n = 82). Differences in chromosomal morphology of some macrochromosomes indicate the presence of intrachromosomal rearrangements. Although the three species only had the 18S rDNA on one microchromosome pair, chromosomal mapping of six simple short repeats revealed a varied pattern of chromosome distribution among them, suggesting that each species underwent different repetitive DNA accumulation upon their divergence. The interspecific comparative genomic hybridization experiment revealed that the Furnariidae species investigated carry centromeric regions enriched in similar repetitive sequences, bolstering the Furnariidae family's karyotype conservation. Nonetheless, the outgroup species Turdus rufiventris (Turdidae) demonstrated an advanced stage of sequence divergence with hybridization signals that were almost entirely limited to a few microchromosomes. Overall, the findings imply that Furnariidae species have a high degree of chromosomal conservation, and we could also observe a differentiation of repetitive sequences in both Passeriformes suborders (Suboscines and Oscines).
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Affiliation(s)
- Victoria Tura
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | | | - Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Vitor Oliveira de Rosso
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | | | - Ricardo J Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
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5
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A near-complete and time-calibrated phylogeny of the Old World flycatchers, robins and chats (Aves, Muscicapidae). Mol Phylogenet Evol 2023; 178:107646. [PMID: 36265831 DOI: 10.1016/j.ympev.2022.107646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recognized genera and ca. 92% of all the species, built using data from up to 15 mitochondrial and 13 nuclear loci. In addition to assembling nucleotide sequences available in public databases, we also extracted sequences from the genome assemblies and raw sequencing reads from GenBank and included a few unpublished sequences. Our analyses resolved the phylogenetic position for several previously unsampled taxa, for example, the Grand Comoro Flycatcher Humblotia flavirostris, the Collared Palm Thrush Cichladusa arquata, and the Taiwan Whistling-Thrush Myophonus insularis, etc. We also provide taxonomic recommendations for genera that exhibit paraphyly or polyphyly. Our results suggest that Muscicapidae diverged from Turdidae (thrushes and allies) in the early Miocene, and the most recent common ancestors for the four subfamilies (Muscicapinae, Niltavinae, Cossyphinae and Saxicolinae) all arose around the middle Miocene.
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6
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Schlenker P, Coye C, Steinert-Threlkeld S, Klinedinst N, Chemla E. Beyond Anthropocentrism in Comparative Cognition: Recentering Animal Linguistics. Cogn Sci 2022; 46:e13220. [PMID: 36479721 DOI: 10.1111/cogs.13220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/06/2022] [Accepted: 10/23/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Philippe Schlenker
- Institut Jean-Nicod (ENS - EHESS - CNRS), Département d'Etudes Cognitives, Ecole Normale Supérieure.,Paris Sciences et Lettres - PSL Research University Paris.,Department of Linguistics, New York University
| | - Camille Coye
- Institut Jean-Nicod (ENS - EHESS - CNRS), Département d'Etudes Cognitives, Ecole Normale Supérieure.,Paris Sciences et Lettres - PSL Research University Paris
| | | | - Nathan Klinedinst
- Division of Psychology and Language Sciences, University College London
| | - Emmanuel Chemla
- Paris Sciences et Lettres - PSL Research University Paris.,LSCP (ENS - EHESS - CNRS), Département d'Etudes Cognitives, Ecole Normale Supérieure
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7
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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8
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Lubbe P, Rawlence NJ, Kardailsky O, Robertson BC, Day R, Knapp M, Dussex N. Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought to have split from their closest relatives outside New Zealand in the Oligocene, but little is known about the timing of divergences within the family. We present a fully dated molecular phylogeny of Callaeidae mitogenomes and discuss the biogeographical implications. Our results suggest that formation of Pliocene marine seaways, such as the Manawatu Strait, are likely to have played a significant role in the differentiation of North Island and South Island kōkako (Callaeas spp.) and saddlebacks/tīeke (Philesturnus spp.).
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Affiliation(s)
- Pascale Lubbe
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Bruce C Robertson
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Robert Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago , Dunedin , New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago , Dunedin , New Zealand
- Coastal People, Southern Skies Centre of Research Excellence, University of Otago , Dunedin , New Zealand
| | - Nicolas Dussex
- Swedish Museum of Natural History, Centre for Palaeogenetics (CPG) , Svante Arrhenius väg, Stockholm , Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm , Sweden
- Department of Zoology, Stockholm University , Stockholm , Sweden
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9
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Dabert J, Mironov SV, Dabert M. The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.
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Affiliation(s)
- Jacek Dabert
- Department of Animal Morphology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego, Poznan, Poland
| | - Serge V Mironov
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment, St. Petersburg, Russia
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego, Poznan, Poland
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10
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Day LB, Helmhout W, Pano G, Olsson U, Hoeksema JD, Lindsay WR. Correlated evolution of acrobatic display and both neural and somatic phenotypic traits in manakins (Pipridae). Integr Comp Biol 2021; 61:1343-1362. [PMID: 34143205 DOI: 10.1093/icb/icab139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/22/2022] Open
Abstract
Brightly colored manakin (Aves: Pipridae) males are known for performing acrobatic displays punctuated by non-vocal sounds (sonations) in order to attract dull colored females. The complexity of the display sequence and assortment of display elements involved (e.g., sonations, acrobatic maneuvers, and cooperative performances) varies considerably across manakin species. Species-specific display elements coevolve with display-distinct specializations of the neuroanatomical, muscular, endocrine, cardiovascular, and skeletal systems in the handful of species studied. Conducting a broader comparative study, we previously found positive associations between display complexity and both brain mass and body mass across 8 manakin genera, indicating selection for neural and somatic expansion to accommodate display elaboration. Whether this gross morphological variation is due to overall brain and body mass expansion (concerted evolution) versus size increases in only functionally relevant brain regions and growth of particular body ("somatic") features (mosaic evolution) remains to be explored. Here we test the hypothesis that cross-species variation in male brain mass and body mass is driven by mosaic evolution. We predicted positive associations between display complexity and variation in the volume of the cerebellum and sensorimotor arcopallium, brain regions which have roles in sensorimotor processes, and learning and performance of precisely timed and sequenced thoughts and movements, respectively. In contrast, we predicted no associations between the volume of a limbic arcopallial nucleus or a visual thalamic nucleus and display complexity as these regions have no-specific functional relationship to display behavior. For somatic features, we predicted that the relationship between body mass and complexity would not include contributions of tarsus length based on a recent study suggesting selection on tarsus length is less labile than body mass. We tested our hypotheses in males from 12 manakin species and a closely related flycatcher. Our analyses support mosaic evolution of neural and somatic features functionally relevant to display and indicate sexual selection for acrobatic complexity may increase the capacity for procedural learning via cerebellar enlargement and maneuverability via a reduction in tarsus length in species with lower overall complexity scores.
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Affiliation(s)
- Lainy B Day
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA.,Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Wilson Helmhout
- Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Glendin Pano
- Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18, SE-413-90 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Jason D Hoeksema
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Willow R Lindsay
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA.,Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18, SE-413-90 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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11
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Ribas TFA, Pieczarka JC, Griffin DK, Kiazim LG, Nagamachi CY, O Brien PCM, Ferguson-Smith MA, Yang F, Aleixo A, O'Connor RE. Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype. BMC Ecol Evol 2021; 21:34. [PMID: 33653261 PMCID: PMC7927240 DOI: 10.1186/s12862-021-01768-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. RESULTS The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. CONCLUSIONS Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.
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Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- School of Biosciences, University of Kent, Canterbury, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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12
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Päckert M, Favre A, Schnitzler J, Martens J, Sun Y, Tietze DT, Hailer F, Michalak I, Strutzenberger P. "Into and Out of" the Qinghai-Tibet Plateau and the Himalayas: Centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds. Ecol Evol 2020; 10:9283-9300. [PMID: 32953061 PMCID: PMC7487248 DOI: 10.1002/ece3.6615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/12/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai-Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one-way street ("out of" the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12-7 Ma). The inferred centers of origin and diversification for some of our target clades matched the "out of Tibet hypothesis' or the "out of Himalayas hypothesis" for others they matched the "into Tibet hypothesis." Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
| | - Adrien Favre
- Entomology IIISenckenberg Research Institute and Natural History Museum FrankfurtFrankfurt am MainGermany
| | - Jan Schnitzler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg‐UniversitätMainzGermany
| | - Yue‐Hua Sun
- Key Laboratory of Animal Ecology and ConservationInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Dieter Thomas Tietze
- Natural History Museum BaselBaselSwitzerland
- Centrum für NaturkundeUniversität HamburgHamburgGermany
| | - Frank Hailer
- School of BiosciencesCardiff UniversityCardiffUK
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Ingo Michalak
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Patrick Strutzenberger
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
- Department of Botany and Biodiversity ResearchUniversität WienWienAustria
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13
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Gajdošová M, Sychra O, Kreisinger J, Sedláček O, Nana ED, Albrecht T, Munclinger P. Patterns of host-parasite associations in tropical lice and their passerine hosts in Cameroon. Ecol Evol 2020; 10:6512-6524. [PMID: 32724529 PMCID: PMC7381757 DOI: 10.1002/ece3.6386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 01/30/2023] Open
Abstract
Coevolutionary processes that drive the patterns of host-parasite associations can be deduced through congruence analysis of their phylogenies. Feather lice and their avian hosts have previously been used as typical model systems for congruence analysis; however, such analyses are strongly biased toward nonpasserine hosts in the temperate zone. Further, in the Afrotropical region especially, cospeciation studies of lice and birds are entirely missing. This work supplements knowledge of host-parasite associations in lice using cospeciation analysis of feather lice (genus Myrsidea and the Brueelia complex) and their avian hosts in the tropical rainforests of Cameroon. Our analysis revealed a limited number of cospeciation events in both parasite groups. The parasite-host associations in both louse groups were predominantly shaped by host switching. Despite a general dissimilarity in phylogeny for the parasites and hosts, we found significant congruence in host-parasite distance matrices, mainly driven by associations between Brueelia lice and passerine species of the Waxbill (Estrildidae) family, and Myrsidea lice and their Bulbul (Pycnonotidae) host species. As such, our study supports the importance of complex biotic interactions in tropical environments.
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Affiliation(s)
- Magdalena Gajdošová
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of EcologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Oldřich Sychra
- Department of Biology and Wildlife DiseasesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Ondřej Sedláček
- Department of EcologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Eric Djomo Nana
- Institute of Agricultural Research for Development (IRAD)Messa ‐YaoundéCameroon
| | - Tomáš Albrecht
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Pavel Munclinger
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
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14
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Riamon S, Tourment N, Louchart A. The earliest Tyrannida (Aves, Passeriformes), from the Oligocene of France. Sci Rep 2020; 10:9776. [PMID: 32555197 PMCID: PMC7299954 DOI: 10.1038/s41598-020-66149-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/12/2020] [Indexed: 11/12/2022] Open
Abstract
Passeriformes is the most diverse bird order. Nevertheless, passerines have a remarkably poor early fossil record. In addition, high osteological homoplasy across passerines makes partial specimens difficult to systematically assign precisely. Here we describe one of the few earliest fossil passerines, from the early Oligocene (ca 30 Ma) of southern France, and one of the best preserved and most complete. This fossil can be conservatively assigned to Tyrannida, a subclade of the New World Tyranni (Suboscines), i.e. of the Tyrannides. A most probably stem-representative of Tyrannida, the new fossil bears strong resemblance with some manakins (Pipridae), possibly due to plesiomorphy. Furthermore, it yields a new point of calibration for molecular phylogenies, already consistent with the age of the fossil. Tyrannida, and the more inclusive Tyrannides, are today confined to the New World. Therefore, the new fossil calls for scenarios of transatlantic crossing during or near the Oligocene. Later, the European part of the distribution of the Tyrannida disappeared, leading to a relictual modern New World distribution of this clade, a pattern known in other avian clades. The history of Tyrannida somehow mirrors that of the enigmatic Sapayoa aenigma, sole New World representative of the Eurylaimides (Old World Tyranni), with transatlantic crossing probably caused by similar events.
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Affiliation(s)
- Ségolène Riamon
- Univ Lyon, Univ Lyon 1, ENSL, CNRS, LGL-TPE, F-69622, Villeurbanne, France
| | | | - Antoine Louchart
- Univ Lyon, Univ Lyon 1, ENSL, CNRS, LGL-TPE, F-69622, Villeurbanne, France.
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15
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de Oliveira TD, Kretschmer R, Bertocchi NÁ, O’Brien PC, Ferguson-Smith MA, Garnero ADV, de Oliveira EHC, Gunski RJ. The molecular cytogenetic characterization of Conopophaga lineata indicates a common chromosome rearrangement in the Parvorder Furnariida (Aves, Passeriformes). Genet Mol Biol 2020; 43:e20200018. [PMID: 32542304 PMCID: PMC7295152 DOI: 10.1590/1678-4685-gmb-2020-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/12/2020] [Indexed: 11/26/2022] Open
Abstract
Cytogenetic analyses of the Suboscines species are still scarce, and so far, there is no karyotype description of any species belonging to the family Conopophagidae. Thus, the aim of this study is to describe and analyze the karyotype of Conopophaga lineata by chromosome painting using Gallus gallus (GGA) probes and to identify the location of the 18/28S rDNA cluster. Metaphases were obtained from fibroblast culture from two individuals of C. lineata. We observed a diploid number of 2n=78. GGA probes showed that most ancestral syntenies are conserved, except for the fission of GGA1 and GGA2, into two distinct pairs each. We identified the location of 18S rDNA genes in a pair of microchromosomes. The fission of the syntenic group corresponding to GGA2 was observed in other Furnariida, and hence may correspond to a chromosomal synapomorphy for the species of Parvorder Furnariida.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Natasha Ávila Bertocchi
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Patricia C.M. O’Brien
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
| | | | - Analía del Valle Garnero
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Instituto Evandro Chagas, Seção Meio Ambiente (SAMAM), Ananindeua, PA, Brazil
- Universidade Federal do Pará, Belém, Instituto de Ciências Exatas e Naturais, Belém, PA, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
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16
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McNab BK, Weston KA. Does the New Zealand rockwren ( Xenicus gilviventris) hibernate? J Exp Biol 2020; 223:jeb212126. [PMID: 32291323 DOI: 10.1242/jeb.212126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/04/2020] [Indexed: 11/20/2022]
Abstract
In this study, we examined the thermal physiology of the endangered New Zealand rockwren (Xenicus gilviventris), a member of the Acanthisittidae, a family unique to New Zealand. This family, derived from Gondwana, is thought to be the sister taxon to all other passerines. Rockwrens permanently reside above the climatic timberline at altitudes from 1000 to 2900 m in the mountains of South Island. They feed on invertebrates and in winter face ambient temperatures far below freezing and deep deposits of snow. Their body temperature and rate of metabolism are highly variable. The rockwrens in our study regulated their body temperature at ca. 36.4°C, which in one individual decreased to 33.1°C at an ambient temperature of 9.4°C; its rate of metabolism decreased by 30% and its body temperature then spontaneously returned to 36°C. The rate of metabolism in a second individual twice decreased by 35%, nearly to the basal rate expected from its mass without a decrease in body temperature. The New Zealand rockwren's food habits, entrance into torpor and continuous residence in a thermally demanding environment suggest that it may hibernate. However, for that conclusion to be accepted, evidence of its use of torpor for extended periods is required. Acanthisittids are distinguished from other passerines by the combination of their permanent temperate distribution, thermal flexibility and a propensity to evolve a flightless condition. These characteristics may principally reflect their geographical isolation in a temperate environment isolated from Gondwana for 82 million years in the absence of mammalian predators.
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Affiliation(s)
- Brian K McNab
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Kerry A Weston
- Biodiversity Group, Department of Conservation, Private Bag 4715, Christchurch Mail Centre, Christchurch 8140, New Zealand
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17
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Olsson U, Alström P. A comprehensive phylogeny and taxonomic evaluation of the waxbills (Aves: Estrildidae). Mol Phylogenet Evol 2020; 146:106757. [PMID: 32028027 DOI: 10.1016/j.ympev.2020.106757] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/23/2019] [Accepted: 01/28/2020] [Indexed: 11/24/2022]
Abstract
We present a revised taxonomy of Estrildidae based on the first time-calibrated phylogeny of the family Estrildidae estimated from a data set including the majority of the species, and all genera except the monospecific Paludipasser, using two mitochondrial and five nuclear markers. We find that most differences in current taxonomy reflect alternative opinions among authors regarding inclusiveness of genera, which are usually not in conflict with the phylogeny. The most notable exception is the current circumscriptions of the genera Neochmia, Nesocharis and Taeniopygia, which are incompatible with the phylogeny. Estrildidae is subdivided into six well supported subclades, which we propose be recognized as the subfamilies Amandavinae, Erythrurinae, Estrildinae, Lagonostictinae, Lonchurinae and Poephilinae.
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Affiliation(s)
- Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden.
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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18
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Batista R, Olsson U, Andermann T, Aleixo A, Ribas CC, Antonelli A. Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history. Proc Biol Sci 2020; 287:20192400. [PMID: 31964299 DOI: 10.1098/rspb.2019.2400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.
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Affiliation(s)
- Romina Batista
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv - Instituto Nacional de Pesquisas da Amazônia (INPA) Campus II, Av. André Araújo, 2936, Petrópolis, CEP 69067-375 Manaus, Amazonas, Brazil.,Coordenação de Zoologia, Laboratório de Biologia Molecular, Museu Paraense Emílio Goeldi, CEP 66077-830 Belém, Pará, Brazil.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
| | - Urban Olsson
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden
| | - Tobias Andermann
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland
| | - Camila Cherem Ribas
- Instituto Nacional de Pesquisas da Amazônia, (INPA) Campus II, Av. André Araújo, 2936, CEP 69060-000 Manaus, Amazonas, Brazil
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden.,Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
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19
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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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20
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Negro JJ, Galván I, Potti J. Adaptive plumage wear for increased crypsis in the plumage of Palearctic larks (Alaudidae). Ecology 2019; 100:e02771. [DOI: 10.1002/ecy.2771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Juan J. Negro
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio 26 Sevilla 41092 Spain
| | - Ismael Galván
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio 26 Sevilla 41092 Spain
| | - Jaime Potti
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio 26 Sevilla 41092 Spain
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21
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Hansson B. On the origin and evolution of germline chromosomes in songbirds. Proc Natl Acad Sci U S A 2019; 116:11570-11572. [PMID: 31142649 PMCID: PMC6575591 DOI: 10.1073/pnas.1906803116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Bengt Hansson
- Department of Biology, Lund University, 223 62 Lund, Sweden
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22
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Slade JWG, Watson MJ, MacDougall‐Shackleton EA. "Balancing" balancing selection? Assortative mating at the major histocompatibility complex despite molecular signatures of balancing selection. Ecol Evol 2019; 9:5146-5157. [PMID: 31110668 PMCID: PMC6509439 DOI: 10.1002/ece3.5087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
Abstract
In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the set of pathogens to which an individual's adaptive immune system can respond. MHC genes are extraordinarily polymorphic, often showing elevated nonsynonymous relative to synonymous sequence variation and sharing presumably ancient polymorphisms between lineages. These patterns likely reflect pathogen-mediated balancing selection, for example, rare-allele or heterozygote advantage. Such selection is often reinforced by disassortative mating at MHC. We characterized exon 2 of MHC class II, corresponding to the hypervariable peptide-binding region, in song sparrows (Melospiza melodia). We compared nonsynonymous to synonymous sequence variation in order to identify positively selected sites; assessed evidence for trans-species polymorphisms indicating ancient balancing selection; and compared MHC similarity of socially mated pairs to expectations under random mating. Six codons showed elevated ratios of nonsynonymous to synonymous variation, consistent with balancing selection, and we characterized several alleles similar to those occurring in at least four other avian families. Despite this evidence for historical balancing selection, mated pairs were significantly more similar at MHC than were randomly generated pairings. Nonrandom mating at MHC thus appears to partially counteract, not reinforce, pathogen-mediated balancing selection in this system. We suggest that in systems where individual fitness does not increase monotonically with MHC diversity, assortative mating may help to avoid excessive offspring heterozygosity that could otherwise arise from long-standing balancing selection.
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Affiliation(s)
- Joel W. G. Slade
- Department of BiologyUniversity of Western OntarioLondonOntarioCanada
| | - Matthew J. Watson
- Department of BiologyUniversity of Western OntarioLondonOntarioCanada
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23
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Abstract
An unusual supernumerary chromosome has been reported for two related avian species, the zebra and Bengalese finches. This large, germline-restricted chromosome (GRC) is eliminated from somatic cells and spermatids and transmitted via oocytes only. Its origin, distribution among avian lineages, and function were mostly unknown so far. Using immunolocalization of key meiotic proteins, we found that GRCs of varying size and genetic content are present in all 16 songbird species investigated and absent from germline genomes of all eight examined bird species from other avian orders. Results of fluorescent in situ hybridization of microdissected GRC probes and their sequencing indicate that GRCs show little homology between songbird species and contain a variety of repetitive elements and unique sequences with paralogs in the somatic genome. Our data suggest that the GRC evolved in the common ancestor of all songbirds and underwent significant changes in the extant descendant lineages.
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24
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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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25
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Hieronymus TL, Waugh DA, Clarke JA. A new zygodactylid species indicates the persistence of stem passerines into the early Oligocene in North America. BMC Evol Biol 2019; 19:3. [PMID: 30611195 PMCID: PMC6321701 DOI: 10.1186/s12862-018-1319-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene - Early Oligocene global cooling in western North America. A nearly complete small bird with feather impressions was recovered from this unit in in 1959, but has only been informally mentioned. RESULTS Here we describe this fossil and identify it as a new species of Zygodactylus, a stem lineage passerine with a zygodactyl foot. The new taxon shows morphological traits that are convergent on crown Passeriformes, including an elongate hallux, reduced body size, and a comparative shortening of proximal limb elements. The fossil documents the persistence of this lineage into the earliest Oligocene (~ 33 Ma) in North America. It is the latest occurring North American species of a group that persists in Europe until the Miocene. CONCLUSIONS Eocene-Oligocene global cooling is known to have significantly remodeled both Palearctic and Nearctic mammal faunas but its impact on related avifaunas has remained poorly understood. The geographic and temporal range expansion provided by the new taxon together with avian other taxa with limited fossil records suggests a similar pattern of retraction in North America followed by Europe.
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Affiliation(s)
- Tobin L. Hieronymus
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Rt 44, Rootstown, OH 44272 USA
| | - David A. Waugh
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Rt 44, Rootstown, OH 44272 USA
| | - Julia A. Clarke
- University of Texas at Austin, Jackson School of Geosciences, Austin, TX USA
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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The energetics of torpor in a temperate passerine endemic to New Zealand, the Rifleman (Acanthisitta chloris). J Comp Physiol B 2018; 188:855-862. [PMID: 30039298 DOI: 10.1007/s00360-018-1175-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/06/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Compared to other birds, passerines, reflecting their small mass, have a narrow set of behavioral characteristics. One difference is that few enter torpor, especially in temperate environments. The few that do include swallows, none of which live throughout the year in cold-temperate environments, because their food, flying insects, is not available in winter and no passerine is known to hibernate. They seasonally migrate to warm-temperate and tropical environments. We present data on the energetics of the Rifleman (Acanthisitta chloris), a small, insectivorous member of the Acanthisittidae, a passerine family endemic to temperate New Zealand. This family is considered to be the sister taxon to all living passerines, which raises the question whether its physiological and behavioral characteristics reflect its evolutionary status in a manner that distinguishes it from other passerines. Only two of the eight known species in this family survive; four of the extinct species were flightless, a condition that evolved independently three times and is almost absent from other passerines. The Rifleman readily enters torpor, which is facilitated by its small mass. It enters torpor at ambient temperatures that are commonly encountered in its wet, cool-to-cold environment. As a result, its body temperature and rate of metabolism are highly variable. An estimate of the basal rate of metabolism is similar to that expected from body mass. Unlike some torpor-prone birds, the Rifleman is a permanent resident in a temperate environment. This residency is possible, because the Rifleman gleans insect prey from surfaces, which does not require insects to have high body temperatures for activity. Its only living relative, the endangered, insectivorous Rock Wren (Xenicus gilviventris), is a permanent resident at altitudes from ca. 1000 to 2500 m in the mountains of South Island, New Zealand. There it faces severe winter conditions that are not avoided by descent to lower altitudes. Its response to these conditions may be an extended period of torpor. The repeated evolution of a flightless condition possibly reflects some distinctive property of the acanthisittids. The evolution of torpor and a flightless condition in acanthisittids may have facilitated their survival on a geographically isolated, temperate landmass, and these character states permitted by the absence of endemic mammalian predators.
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Russo CADM, Selvatti AP. Bootstrap and Rogue Identification Tests for Phylogenetic Analyses. Mol Biol Evol 2018; 35:2327-2333. [DOI: 10.1093/molbev/msy118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Claudia Augusta de Moraes Russo
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro CCS, Ilha do Fundão, Rio de Janeiro, Brazil
| | - Alexandre Pedro Selvatti
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro CCS, Ilha do Fundão, Rio de Janeiro, Brazil
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Mate sampling influences the intensity of sexual selection and the evolution of costly sexual ornaments. J Theor Biol 2018; 447:74-83. [PMID: 29567325 DOI: 10.1016/j.jtbi.2018.03.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/30/2018] [Accepted: 03/19/2018] [Indexed: 11/20/2022]
Abstract
Mate choice includes three steps: (1) a choosing individual encounters potential mates, (2) assesses and processes information about them, and (3) makes a mate decision. During mate searching females can access only a sample of males in the mating pool and need to choose their mates based on limited information. Thus, mate sampling may influence sexual selection promoted by mate choice because it constrains female choice. Using individual-based simulations, we found that both female choosiness and mate sampling influenced the variance in mating success among males and thus the intensity of sexual selection. So that sexual selection is most intense when females are strongly choosy and can sample many males. Moreover, in evolutionary simulations, the rate of evolutionary change and the final size of male ornament increase with increasing mate sampling. However, under stronger natural selection, evolutionary change is slower and leads to smaller ornaments. Empirical data on the potential for sexual selection (Is) for several animal species show a positive correlation between the intensity of sexual selection and an index of mate sampling based on behavioral and ecological traits. Based on the results of our simulations, we predict that males of highly mobile species with long-range sexual signal transmission, which allow females to assess many males, will show greater variance in mating success and will be more ornamented than their relatives not exhibiting these features.
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Kretschmer R, de Lima VLC, de Souza MS, Costa AL, O’Brien PCM, Ferguson-Smith MA, de Oliveira EHC, Gunski RJ, Garnero ADV. Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions. COMPARATIVE CYTOGENETICS 2018; 12:97-110. [PMID: 29675139 PMCID: PMC5904361 DOI: 10.3897/compcytogen.v12i1.22344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Vanusa Lilian Camargo de Lima
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Marcelo Santos de Souza
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Alice Lemos Costa
- Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Patricia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
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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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Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis). G3-GENES GENOMES GENETICS 2017; 7:3983-3998. [PMID: 29054864 PMCID: PMC5714495 DOI: 10.1534/g3.117.300152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)—two recently diverged species which differ in morphology, plumage, song, habitat, and migration—to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.
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Hasegawa M, Kuroda S. Phylogeny mandalas of birds using the lithographs of John Gould’s folio bird books. Mol Phylogenet Evol 2017; 117:141-149. [DOI: 10.1016/j.ympev.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022]
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The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies. Mol Phylogenet Evol 2017; 116:69-77. [DOI: 10.1016/j.ympev.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/03/2017] [Accepted: 08/06/2017] [Indexed: 11/22/2022]
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Smith EK, O'Neill JJ, Gerson AR, McKechnie AE, Wolf BO. Avian thermoregulation in the heat: resting metabolism, evaporative cooling and heat tolerance in Sonoran Desert songbirds. ACTA ACUST UNITED AC 2017; 220:3290-3300. [PMID: 28684465 DOI: 10.1242/jeb.161141] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/04/2017] [Indexed: 11/20/2022]
Abstract
We examined thermoregulatory performance in seven Sonoran Desert passerine bird species varying in body mass from 10 to 70 g - lesser goldfinch, house finch, pyrrhuloxia, cactus wren, northern cardinal, Abert's towhee and curve-billed thrasher. Using flow-through respirometry, we measured daytime resting metabolism, evaporative water loss and body temperature at air temperatures (Tair) between 30 and 52°C. We found marked increases in resting metabolism above the upper critical temperature (Tuc), which for six of the seven species fell within a relatively narrow range (36.2-39.7°C), but which was considerably higher in the largest species, the curve-billed thrasher (42.6°C). Resting metabolism and evaporative water loss were minimal below the Tuc and increased with Tair and body mass to maximum values among species of 0.38-1.62 W and 0.87-4.02 g H2O h-1, respectively. Body temperature reached maximum values ranging from 43.5 to 45.3°C. Evaporative cooling capacity, the ratio of evaporative heat loss to metabolic heat production, reached maximum values ranging from 1.39 to 2.06, consistent with known values for passeriforms and much lower than values in taxa such as columbiforms and caprimulgiforms. These maximum values occurred at heat tolerance limits that did not scale with body mass among species, but were ∼50°C for all species except the pyrrhuloxia and Abert's towhee (48°C). High metabolic costs associated with respiratory evaporation appeared to drive the limited heat tolerance in these desert passeriforms, compared with larger desert columbiforms and galliforms that use metabolically more efficient mechanisms of evaporative heat loss.
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Affiliation(s)
- Eric Krabbe Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Alexander R Gerson
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.,Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Andrew E McKechnie
- DST-NRF Centre of Excellence at the Percy FitzPatrick Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa
| | - Blair O Wolf
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Corlett RT. Frugivory and seed dispersal by vertebrates in tropical and subtropical Asia: An update. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.04.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Selvatti AP, Galvão A, Pereira AG, Pedreira Gonzaga L, Russo CADM. An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae). Mol Biol Evol 2017; 34:483-499. [PMID: 28069777 DOI: 10.1093/molbev/msw250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.
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Affiliation(s)
- Alexandre Pedro Selvatti
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Ana Galvão
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anieli Guirro Pereira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Luiz Pedreira Gonzaga
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Worthy TH, De Pietri VL, Scofield RP. Recent advances in avian palaeobiology in New Zealand with implications for understanding New Zealand’s geological, climatic and evolutionary histories. NEW ZEALAND JOURNAL OF ZOOLOGY 2017. [DOI: 10.1080/03014223.2017.1307235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Trevor H. Worthy
- School of Biological Sciences, Flinders University of South Australia, GPO 2100, Adelaide 5001, South Australia
| | - Vanesa L. De Pietri
- Natural History Department, Canterbury Museum, Rolleston Avenue, Christchurch 8013, New Zealand
| | - R. Paul Scofield
- Natural History Department, Canterbury Museum, Rolleston Avenue, Christchurch 8013, New Zealand
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Affiliation(s)
- Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Marco Crotti
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
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Cai L, Xi Z, Peterson K, Rushworth C, Beaulieu J, Davis CC. Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade. PLoS One 2016; 11:e0161881. [PMID: 27684711 PMCID: PMC5042423 DOI: 10.1371/journal.pone.0161881] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/12/2016] [Indexed: 01/31/2023] Open
Abstract
The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions.
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Affiliation(s)
- Liming Cai
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States of America
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States of America
| | - Kylee Peterson
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States of America
| | - Catherine Rushworth
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States of America
| | - Jeremy Beaulieu
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, United States of America
- * E-mail:
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Hosner PA, Braun EL, Kimball RT. Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences. Mol Phylogenet Evol 2016; 102:320-30. [DOI: 10.1016/j.ympev.2016.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 01/29/2023]
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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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Sobral G, Müller J. Archosaurs and Their Kin: The Ruling Reptiles. EVOLUTION OF THE VERTEBRATE EAR 2016. [DOI: 10.1007/978-3-319-46661-3_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Frazão A, da Silva HR, Russo CADM. The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification. PLoS One 2015; 10:e0143926. [PMID: 26618546 PMCID: PMC4664409 DOI: 10.1371/journal.pone.0143926] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/11/2015] [Indexed: 11/20/2022] Open
Abstract
The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.
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Affiliation(s)
- Annelise Frazão
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hélio Ricardo da Silva
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Claudia Augusta de Moraes Russo
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Jønsson KA, Fabre PH, Kennedy JD, Holt BG, Borregaard MK, Rahbek C, Fjeldså J. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides). Mol Phylogenet Evol 2015; 94:87-94. [PMID: 26327328 DOI: 10.1016/j.ympev.2015.08.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/30/2015] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not.
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Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark; Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Jonathan D Kennedy
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Ben G Holt
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark; Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
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