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Widrig KE, Navalón G, Field DJ. Paleoneurology of stem palaeognaths clarifies the plesiomorphic condition of the crown bird central nervous system. J Morphol 2024; 285:e21710. [PMID: 38760949 DOI: 10.1002/jmor.21710] [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: 04/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
Lithornithidae, an assemblage of volant Palaeogene fossil birds, provide our clearest insights into the early evolutionary history of Palaeognathae, the clade that today includes the flightless ratites and volant tinamous. The neotype specimen of Lithornis vulturinus, from the early Eocene (approximately 53 million years ago) of Europe, includes a partial neurocranium that has never been thoroughly investigated. Here, we describe these cranial remains including the nearly complete digital endocasts of the brain and bony labyrinth. The telencephalon of Lithornis is expanded and its optic lobes are ventrally shifted, as is typical for crown birds. The foramen magnum is positioned caudally, rather than flexed ventrally as in some crown birds, with the optic lobes, cerebellum, and foramen magnum shifted further ventrally. The overall brain shape is similar to that of tinamous, the only extant clade of flying palaeognaths, suggesting that several aspects of tinamou neuroanatomy may have been evolutionarily conserved since at least the early Cenozoic. The estimated ratio of the optic lobe's surface area relative to the total brain suggests a diurnal ecology. Lithornis may provide the clearest insights to date into the neuroanatomy of the ancestral crown bird, combining an ancestrally unflexed brain with a caudally oriented connection with the spinal cord, a moderately enlarged telencephalon, and ventrally shifted, enlarged optic lobes.
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Affiliation(s)
- Klara E Widrig
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Guillermo Navalón
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
- Fossil Reptiles, Amphibians and Birds Section, The Natural History Museum, London, UK
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2
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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3
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Peacock J, Spellman GM, Field DJ, Mason MJ, Mayr G. Comparative morphology of the avian bony columella. Anat Rec (Hoboken) 2024; 307:1735-1763. [PMID: 37365751 DOI: 10.1002/ar.25278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
In birds, the columella is the only bony element of the sound conducting apparatus, conveying vibrations of the cartilaginous extracolumella to the fluid of the inner ear. Although avian columellar morphology has attracted some attention over the past century, it nonetheless remains poorly described in the literature. The few existing studies mostly focus on morphological descriptions in relatively few taxa, with no taxonomically broad surveys yet published. Here we use observations of columellae from 401 extant bird species to provide a comprehensive survey of columellar morphology in a phylogenetic context. We describe the columellae of several taxa for the first time and identify derived morphologies characterizing higher-level clades based on current phylogenies. In particular, we identify a derived columellar morphology diagnosing a major subclade of Accipitridae. Within Suliformes, we find that Fregatidae, Sulidae, and Phalacrocoracidae share a derived morphology that is absent in Anhingidae, suggesting a secondary reversal. Phylogenetically informed comparisons allow recognition of instances of homoplasy, including the distinctive bulbous columellae in suboscine passerines and taxa belonging to Eucavitaves, and bulging footplates that appear to have evolved at least twice independently in Strigiformes. We consider phylogenetic and functional factors influencing avian columellar morphology, finding that aquatic birds possess small footplates relative to columellar length, possibly related to hearing function in aquatic habitats. By contrast, the functional significance of the distinctive bulbous basal ends of the columellae of certain arboreal landbird taxa remains elusive.
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Affiliation(s)
- John Peacock
- Department of Physiology and Biophysics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature and Science, Denver, Colorado, USA
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
| | - Matthew J Mason
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
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4
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Brownstein CD. A juvenile bird with possible crown-group affinities from a dinosaur-rich Cretaceous ecosystem in North America. BMC Ecol Evol 2024; 24:20. [PMID: 38336630 PMCID: PMC10858573 DOI: 10.1186/s12862-024-02210-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Living birds comprise the most speciose and anatomically diverse clade of flying vertebrates, but their poor early fossil record and the lack of resolution around the relationships of the major clades have greatly obscured extant avian origins. RESULTS Here, I describe a Late Cretaceous bird from North America based on a fragmentary skeleton that includes cranial material and portions of the forelimb, hindlimb, and foot and is identified as a juvenile based on bone surface texture. Several features unite this specimen with crown Aves, but its juvenile status precludes the recognition of a distinct taxon. The North American provenance of the specimen supports a cosmopolitan distribution of early crown birds, clashes with the hypothesized southern hemisphere origins of living birds, and demonstrates that crown birds and their closest relatives coexisted with non-avian dinosaurs that independently converged on avian skeletal anatomy, such as the alvarezsaurids and dromaeosaurids. CONCLUSIONS By revealing the ecological and biogeographic context of Cretaceous birds within or near the crown clade, the Lance Formation specimen provides new insights into the contingent nature of crown avian survival through the Cretaceous-Paleogene mass extinction and the subsequent origins of living bird diversity.
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Affiliation(s)
- Chase Doran Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
- , Stamford, USA.
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Longtine C, Eliason CM, Mishkind D, Lee C, Chiappone M, Goller F, Love J, Kingsley EP, Clarke JA, Tabin CJ. Homology and the evolution of vocal folds in the novel avian voice box. Curr Biol 2024; 34:461-472.e7. [PMID: 38183987 DOI: 10.1016/j.cub.2023.12.013] [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: 06/14/2023] [Revised: 08/29/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
The origin of novel traits, those that are not direct modifications of a pre-existing ancestral structure, remains a fundamental problem in evolutionary biology. For example, little is known about the evolutionary and developmental origins of the novel avian vocal organ, the syrinx. Located at the tracheobronchial junction, the syrinx is responsible for avian vocalization, but it is unclear whether avian vocal folds are homologous to the laryngeal vocal folds in other tetrapods or convergently evolved. Here, we identify a core developmental program involved in avian vocal fold formation and infer the morphology of the syrinx of the ancestor of modern birds. We find that this ancestral syrinx had paired sound sources induced by a conserved developmental pathway and show that shifts in these signals correlate with syringeal diversification. We show that, despite being derived from different developmental tissues, vocal folds in the syrinx and larynx have similar tissue composition and are established through a strikingly similar developmental program, indicating that co-option of an ancestral developmental program facilitated the origin of vocal folds in the avian syrinx.
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Affiliation(s)
- Charlie Longtine
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chad M Eliason
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Darcy Mishkind
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Chiappone
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Franz Goller
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; Department of Zoophysiology, University of Münster, 48149 Münster, Germany
| | - Jay Love
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Evan P Kingsley
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Julia A Clarke
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Lan G, Yu J, Liu J, Zhang Y, Ma R, Zhou Y, Zhu B, Wei W, Liu J, Qi G. Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae). Genes (Basel) 2024; 15:90. [PMID: 38254979 PMCID: PMC10815732 DOI: 10.3390/genes15010090] [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: 11/09/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
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Affiliation(s)
- Guanwei Lan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Juan Liu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Yue Zhang
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Biqing Zhu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guilan Qi
- Animal Husbandry Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
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Henríquez-Piskulich P, Hugall AF, Stuart-Fox D. A supermatrix phylogeny of the world's bees (Hymenoptera: Anthophila). Mol Phylogenet Evol 2024; 190:107963. [PMID: 37967640 DOI: 10.1016/j.ympev.2023.107963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
The increasing availability of large molecular phylogenies has provided new opportunities to study the evolution of species traits, their origins and diversification, and biogeography; yet there are limited attempts to synthesise existing phylogenetic information for major insect groups. Bees (Hymenoptera: Anthophila) are a large group of insect pollinators that have a worldwide distribution, and a wide variation in ecology, morphology, and life-history traits, including sociality. For these reasons, as well as their major economic importance as pollinators, numerous molecular phylogenetic studies of family and genus-level relationships have been published, providing an opportunity to assemble a bee 'tree-of-life'. We used publicly available genetic sequence data, including phylogenomic data, reconciled to a taxonomic database, to produce a concatenated supermatrix phylogeny for the Anthophila comprising 4,586 bee species, representing 23% of species and 82% of genera. At family, subfamily, and tribe levels, support for expected relationships was robust, but between and within some genera relationships remain uncertain. Within families, sampling of genera ranged from 67 to 100% but species coverage was lower (17-41%). Our phylogeny mostly reproduces the relationships found in recent phylogenomic studies with a few exceptions. We provide a summary of these differences and the current state of molecular data available and its gaps. We discuss the advantages and limitations of this bee supermatrix phylogeny (available online at beetreeoflife.org), which may enable new insights into long standing questions about evolutionary drivers in bees, and potentially insects more generally.
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Affiliation(s)
| | - Andrew F Hugall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia; Department of Sciences, Museums Victoria, Melbourne, Victoria, Australia.
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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8
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Widrig KE, Bhullar BS, Field DJ. 3D atlas of tinamou (Neornithes: Tinamidae) pectoral morphology: Implications for reconstructing the ancestral neornithine flight apparatus. J Anat 2023; 243:729-757. [PMID: 37358291 PMCID: PMC10557402 DOI: 10.1111/joa.13919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
Palaeognathae, the extant avian clade comprising the flightless ratites and flight-capable tinamous (Tinamidae), is the sister group to all other living birds, and recent phylogenetic studies illustrate that tinamous are phylogenetically nested within a paraphyletic assemblage of ratites. As the only extant palaeognaths that have retained the ability to fly, tinamous may provide key information on the nature of the flight apparatus of ancestral crown palaeognaths-and, in turn, crown birds-as well as insight into convergent modifications to the wing apparatus among extant ratite lineages. To reveal new information about the musculoskeletal anatomy of tinamous and facilitate development of computational biomechanical models of tinamou wing function, we generated a three-dimensional musculoskeletal model of the flight apparatus of the extant Andean tinamou (Nothoprocta pentlandii) using diffusible iodine-based contrast-enhanced computed tomography (diceCT). Origins and insertions of the pectoral flight musculature of N. pentlandii are generally consistent with those of other extant volant birds specialized for burst flight, and the entire suite of presumed ancestral neornithine flight muscles are present in N. pentlandii with the exception of the biceps slip. The pectoralis and supracoracoideus muscles are robust, similar to the condition in other extant burst-flying birds such as many extant Galliformes. Contrary to the condition in most extant Neognathae (the sister clade to Palaeognathae), the insertion of the pronator superficialis has a greater distal extent than the pronator profundus, although most other anatomical observations are broadly consistent with the conditions observed in extant neognaths. This work will help form a basis for future comparative studies of the avian musculoskeletal system, with implications for reconstructing the flight apparatus of ancestral crown birds and clarifying musculoskeletal modifications underlying the convergent origins of ratite flightlessness.
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Affiliation(s)
- Klara E. Widrig
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Bhart‐Anjan S. Bhullar
- Department of Earth and Planetary SciencesYale UniversityNew HavenConnecticutUSA
- Peabody Museum of Natural HistoryYale UniversityNew HavenConnecticutUSA
| | - Daniel J. Field
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- Museum of ZoologyUniversity of CambridgeCambridgeUK
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9
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Claramunt S, Haddrath O. No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds. Genome Biol Evol 2023; 15:evad173. [PMID: 37758449 PMCID: PMC10563790 DOI: 10.1093/gbe/evad173] [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: 06/18/2023] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023] Open
Abstract
Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.
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Affiliation(s)
- Santiago Claramunt
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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10
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Skoracki M, Fajfer M, Hromada M, Hušek J, Sikora B. Tinamiphilopsis temmincki sp. n., a New Quill Mite Species from Tataupa Tinamou, and the Early History of Syringophilid Mites. Animals (Basel) 2023; 13:2728. [PMID: 37684992 PMCID: PMC10486729 DOI: 10.3390/ani13172728] [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: 07/03/2023] [Revised: 07/24/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The quill mite fauna of the Syringophilidae family (Acariformes: Prostigmata), which is associated with palaeognathous birds of the Tinamiformes order, remains poorly studied. Thus far, only two species of syringophilid mites have been documented on four species of tinamous. In this study, we present a description of a new species, Tinamiphilopsis temmincki sp. n., which was found on the Tataupa Tinamou (Crypturellus tataupa) in South America. This newly identified species differs from others in the genus due to the short hysteronotal setae d2 in females, unlike the long setae d2 found in females of other Tinamiphilopsis species. In addition to describing the new species, we conducted a phylogenetic analysis of the primitive syringophilid genera. The results reveal that the Tinamiphilopsis genus does not emerge as a sister group to all other syringophilids. Instead, it is deeply embedded within the radiation of quill mites associated with neognathous birds. This study provided evidence that mites belonging to the genus Tinamiphilopsis initially parasitised Neoavian birds before host switching to tinamous birds. This placement carries significant implications for our understanding of the evolution of quill mites and their relationship with their avian hosts.
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Affiliation(s)
- Maciej Skoracki
- Department of Animal Morphology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Monika Fajfer
- Department of Molecular Biology and Genetics, Institute of Biological Sciences, Cardinal Stefan Wyszynski University, Wóycickiego 1/3, 01-938 Warsaw, Poland;
| | - Martin Hromada
- Laboratory and Museum of Evolutionary Ecology, Department of Ecology, Faculty of Humanities and Natural Sciences, University of Prešov, 08001 Prešov, Slovakia;
| | - Jan Hušek
- National Museum of the Czech Republic, Václavské námestí 68, 11579 Prague, Czech Republic;
| | - Bozena Sikora
- Department of Animal Morphology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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11
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Gutiérrez-Ibáñez C, Amaral-Peçanha C, Iwaniuk AN, Wylie DR, Baron J. Online repositories of photographs and videos provide insights into the evolution of skilled hindlimb movements in birds. Commun Biol 2023; 6:781. [PMID: 37582975 PMCID: PMC10427617 DOI: 10.1038/s42003-023-05151-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
The ability to manipulate objects with limbs has evolved repeatedly among land tetrapods. Several selective forces have been proposed to explain the emergence of forelimb manipulation, however, work has been largely restricted to mammals, which prevents the testing of evolutionary hypotheses in a comprehensive evolutionary framework. In birds, forelimbs have gained the exclusive function of flight, with grasping transferred predominantly to the beak. In some birds, the feet are also used in manipulative tasks and appear to share some features with manual grasping and prehension in mammals, but this has not been systematically investigated. Here we use large online repositories of photographs and videos to quantify foot manipulative skills across a large sample of bird species (>1000 species). Our results show that a complex interaction between niche, diet and phylogeny drive the evolution of manipulative skills with the feet in birds. Furthermore, we provide strong support for the proposition that an arboreal niche is a key element in the evolution of manipulation in land vertebrates. Our systematic comparison of foot use in birds provides a solid base for understanding morphological and neural adaptations for foot use in birds, and for studying the convergent evolution of manipulative skills in birds and mammals.
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Affiliation(s)
| | - Clara Amaral-Peçanha
- Graduate Program in Physiology and Pharmacology Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrew N Iwaniuk
- Department of Neuroscience, Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alta., Canada
| | - Douglas R Wylie
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Jerome Baron
- Graduate Program in Physiology and Pharmacology Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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12
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Basal Anseriformes from the Early Paleogene of North America and Europe. DIVERSITY 2023. [DOI: 10.3390/d15020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We describe nearly complete skeletons of basal Anseriformes from the Latest Paleocene to the early Eocene of North America and Europe. Collectively, these birds appear to be representative of anseriforms near the divergence of Anhimae and Anseres, but their exact positions relative to these clades remains uncertain. A new family, Anachronornithidae nov. fam., is erected on the basis of one of these, Anachronornis anhimops nov. gen., nov. gen. et sp., to which the others cannot be confidently assigned. The new fossils augment a growing collection of early Pan-Anseriformes, which in their diversity do not paint an unambiguous picture of phylogeny or character state evolution on the path to or within crown-Anseriformes. Anachronornis nov. gen. is similar in some aspects of both cranial and postcranial anatomy to other well-represented early Paleogene Anseriformes and members of Anseres, such as Presbyornis Wetmore, 1926. However, it exhibits a more landfowl-like bill, like that of Anhimae and unlike the spatulate bill of Anseres. Additional specimens of similar basal Anseriformes of uncertain affinities from the early Eocene of North America and Europe further complicate interpretation of character state polarity due to the mosaicism of primitive and derived characters they exhibit.
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Choi S, Hauber ME, Legendre LJ, Kim NH, Lee YN, Varricchio DJ. Microstructural and crystallographic evolution of palaeognath (Aves) eggshells. eLife 2023; 12:e81092. [PMID: 36719067 PMCID: PMC9889092 DOI: 10.7554/elife.81092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/11/2022] [Indexed: 02/01/2023] Open
Abstract
The avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).
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Affiliation(s)
- Seung Choi
- Department of Earth Sciences, Montana State UniversityBozemanUnited States
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois Urbana-ChampaignUrbanaUnited States
| | - Lucas J Legendre
- Department of Geological Sciences, University of Texas at AustinAustinUnited States
| | - Noe-Heon Kim
- School of Earth and Environmental Sciences, Seoul National UniversitySeoulRepublic of Korea
- Department of Geosciences, Princeton UniversityPrincetonUnited States
| | - Yuong-Nam Lee
- School of Earth and Environmental Sciences, Seoul National UniversitySeoulRepublic of Korea
| | - David J Varricchio
- Department of Earth Sciences, Montana State UniversityBozemanUnited States
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14
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Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science 2023; 379:185-190. [PMID: 36634192 DOI: 10.1126/science.abn7050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.
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Affiliation(s)
- Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Tom Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Keren Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Andrea H Gaede
- University of British Columbia, Vancouver, Vancouver, BC V6T 1Z4, Canada.,Structure and Motion Laboratory, Royal Veterinary College, University of London, London, UK
| | - Amanda Monte
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Julia Jarrells
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Marc Bickle
- Roche Institute for Translational Bioengineering, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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15
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McKone MJ. Loss of Avian Intromittent Organs as a Sperm Competition Strategy: A Race to Be Last. Am Nat 2023; 201:138-153. [PMID: 36524937 DOI: 10.1086/722100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe loss of the intromittent organ (IO) in the majority of birds remains unexplained. Here, I propose that IO loss results from sperm competition in the context of the unique avian sperm storage system. The first stage of fertilization is the movement of sperm through the vagina from the site of ejaculation to the sperm storage tubules (SSTs) at the uterovaginal junction. In a second stage, sperm are released from the SSTs and move through the uterus to the site of fertilization in the infundibulum. Last-male fertilization precedence can occur if sperm that arrive later at the uterovaginal junction occupy uterus-side SSTs, which then have a head start in the race to the infundibulum with each ovulation. Under such "last-in, first-out" conditions, there is strong sperm competition to arrive later at the SSTs. Consequently, the optimal male strategy would be placement of the ejaculate at the cloacal opening to allow any other sperm in the vagina to reach the SSTs first. Cloacal placement is effectively achieved by loss of the IO. The evolution of altricial development in Neoaves, the largest clade that lacks IOs, created conditions that favor IO loss. Specifically, the smaller clutch sizes and hatching asynchrony of altricial birds increase the intensity of sperm competition for fertilization of early eggs in the laying sequence and thus the selective advantage of later arrival at the SSTs. The rarity of IO loss among all animals suggests that the complex mechanism of avian fertilization creates unique conditions for sperm competition.
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16
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Host-Parasite Relationships of Quill Mites (Syringophilidae) and Parrots (Psittaciformes). DIVERSITY 2022. [DOI: 10.3390/d15010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The family Syringophilidae (Acari: Prostigmata) includes obligatory ectoparasites, which occupy feather quills from various parts of avian plumage, where they feed and reproduce. Our study was concerned with the global fauna of syringophilid mites associated with Psittaciformes, as well as host-parasite specificity and evolution. We assumed that the system composed of quill mites and parrots represents a model group that can be used in a broader study of the relationships between parasites and hosts. In total, we examined 1524 host individuals of parrots belonging to 195 species, 73 genera, and 4 families (which constitute ca. 50% of global parrot fauna) from all zoogeographical regions where Psittaciformes occur. Among them, 89 individuals representing 81 species have been infested by quill mites belonging to 45 species and 8 genera. The prevalence of host infestations by syringophilid mites varied from 2.8% to 100% (95% confidence interval (CI Sterne method) = 0.1–100). We applied a bipartite analysis to determine the parasite-host interaction, network indices, and host specificity at the species and whole network levels. The Syringophilidae-Psittaciformes network was composed of 24 mite species and 47 host species. The bipartite network was characterized by a high network level specialization H2′ = 0.98, connectance C = 0.89, and high modularity Q = 0.90, with 23 modules, but low nestedness N = 0.0333. Moreover, we reconstructed the phylogeny of the quill mites on the generic level, and this analysis shows two distinct clades: Psittaciphilus (Peristerophila + Terratosyringophilus) (among Syringophilinae subfamily) and Lawrencipicobia (Pipicobia + Rafapicobia) (among Picobiinae). Finally, the distributions and host-parasite relationships in the system composed of syringophilid mites and parrots are discussed.
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The endocast of the insular and extinct Sylviornis neocaledoniae (Aves, Galliformes), reveals insights into its sensory specializations and its twilight ecology. Sci Rep 2022; 12:21185. [PMID: 36477415 PMCID: PMC9729198 DOI: 10.1038/s41598-022-14829-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
Sylviornis neocaledoniae (Galliformes, Sylviornithidae), a recently extinct bird of New-Caledonia (Galliformes, Sylviornithidae) is the largest galliform that ever lived and one of the most enigmatic birds in the world. Herein, for the first time, we analyze its neuroanatomy that sheds light on its lifestyle, its brain shape and patterns being correlated to neurological functions. Using morphometric methods, we quantified the endocranial morphology of S. neocaledoniae and compared it with extinct and extant birds in order to obtain ecological and behavioral information about fossil birds. Sylviornis neocaledoniae exhibited reduced optic lobes, a condition also observed in nocturnal taxa endemic to predator-depauperate islands, such as Elephant birds. Functional interpretations suggest that S. neocaledoniae possessed a well-developed somatosensorial system and a good sense of smell in addition to its specialized visual ability for low light conditions, presumably for locating its food. We interpret these results as evidence for a crepuscular lifestyle in S. neocaledoniae.
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Pelegrin JS, Cantalapiedra JL, Gamboa S, Menéndez I, Hernández Fernández M. Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for the first time, the evolution of biome occupation in birds. We aimed to analyse patterns of adaptation to different climatic regimes and the determinant factors for colonization of emerging biomes by clades from different ancestral biomes. In this work, we reconstructed the biome occupation history of two clades of birds (Galliformes and Falconiformes) under an integrative perspective through a comprehensive review of ecological, phylogenetic, palaeontological and biogeographical evidence. Our findings for both groups are consistent with a scenario of phylogenetic biome conservatism and highlight the importance of changes in climate during the Miocene in the adaptation and evolution of climatic niches. In particular, our results indicate high biome conservatism associated with biomes situated in some of the extremes of the global climate gradient (evergreen tropical rainforest, steppe and tundra) for both bird taxa. Finally, the historical dynamics of tropical seasonal biomes, such as tropical deciduous woodlands and savannas, appear to have played a preponderant role during the diversification processes of these bird lineages.
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Affiliation(s)
- Jonathan S Pelegrin
- Grupo de Investigación en Ecología y Conservación de la Biodiversidad (EcoBio), Área de Biología y Programa de Maestría en Educación Ambiental y Desarrollo Sostenible, Facultades de Ciencias Básicas y Educación, Universidad Santiago de Cali , Colombia
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle , Colombia
| | - Juan L Cantalapiedra
- GloCEE – Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá , 28805, Alcalá de Henares (Madrid ), Spain
| | - Sara Gamboa
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Iris Menéndez
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Manuel Hernández Fernández
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
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Cramer JF, Miller ET, Ko MC, Liang Q, Cockburn G, Nakagita T, Cardinale M, Fusani L, Toda Y, Baldwin MW. A single residue confers selective loss of sugar sensing in wrynecks. Curr Biol 2022; 32:4270-4278.e5. [PMID: 35985327 DOI: 10.1016/j.cub.2022.07.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.1-3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage's evolutionary history,4 subsequent shifts in a species' behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.5-7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.8,9 Our analyses show that, similar to hummingbirds10 and songbirds,4 the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.
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Affiliation(s)
- Julia F Cramer
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Eliot T Miller
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY 14850, USA
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Qiaoyi Liang
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Massimiliano Cardinale
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, 453 30 Lysekil, Sweden
| | - Leonida Fusani
- Austrian Ornithological Centre, Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, 1160 Wien, Austria; Department of Behavioural and Cognitive Biology, University of Vienna, 1160 Wien, Austria
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
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20
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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Adenoviruses in Avian Hosts: Recent Discoveries Shed New Light on Adenovirus Diversity and Evolution. Viruses 2022; 14:v14081767. [PMID: 36016389 PMCID: PMC9416666 DOI: 10.3390/v14081767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
While adenoviruses cause infections in a wide range of vertebrates, members of the genus Atadenovirus, Siadenovirus, and Aviadenovirus predominantly infect avian hosts. Several recent studies on avian adenoviruses have encouraged us to re-visit previously proposed adenovirus evolutionary concepts. Complete genomes and partial DNA polymerase sequences of avian adenoviruses were extracted from NCBI and analysed using various software. Genomic analyses and constructed phylogenetic trees identified the atadenovirus origin from an Australian native passerine bird in contrast to the previously established reptilian origin. In addition, we demonstrated that the theories on higher AT content in atadenoviruses are no longer accurate and cannot be considered as a species demarcation criterion for the genus Atadenovirus. Phylogenetic reconstruction further emphasised the need to reconsider siadenovirus origin, and we recommend extended studies on avian adenoviruses in wild birds to provide finer evolutionary resolution.
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Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
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The Application of Quantitative Metabolomics for the Taxonomic Differentiation of Birds. BIOLOGY 2022; 11:biology11071089. [PMID: 36101467 PMCID: PMC9312993 DOI: 10.3390/biology11071089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022]
Abstract
In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski's bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life.
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Gatesy J, Springer MS. Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves. Genes (Basel) 2022; 13:genes13071167. [PMID: 35885951 PMCID: PMC9324441 DOI: 10.3390/genes13071167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous−Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species−tree inference.
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Affiliation(s)
- John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Correspondence:
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA;
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Wang N, Braun EL, Liang B, Cracraft J, Smith SA. Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree. Mol Phylogenet Evol 2022; 174:107550. [PMID: 35691570 DOI: 10.1016/j.ympev.2022.107550] [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: 07/29/2020] [Revised: 05/13/2022] [Accepted: 06/02/2022] [Indexed: 11/28/2022]
Abstract
Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GCCV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding) per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and vultures). Eliminating high GCCV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.
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Affiliation(s)
- Ning Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA.
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Bin Liang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA
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Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome assembly and evolutionary analysis of the mandarin duck Aix galericulata reveal strong genome conservation among ducks. Genome Biol Evol 2022; 14:6594746. [PMID: 35640266 PMCID: PMC9189614 DOI: 10.1093/gbe/evac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3–26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Pin-Chi Tang
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Hsu-Chen Cheng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, USA
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Wang J, Su W, Hu Y, Li S, O'Brien PCM, Ferguson-Smith MA, Yang F, Nie W. Comparative chromosome maps between the stone curlew and three ciconiiform species (the grey heron, little egret and crested ibis). BMC Ecol Evol 2022; 22:23. [PMID: 35240987 PMCID: PMC8892796 DOI: 10.1186/s12862-022-01979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Previous cytogenetic studies show that the karyotypes of species in Ciconiiformes vary considerably, from 2n = 52 to 78. Their karyotypes include different numbers of small to minute bi-armed chromosomes that have evolved probably by fusions of two ancestral microchromosomes, besides macrochromosomes and dot-like microchromosomes. However, it is impossible to define the inter-species homologies of such small-sized bi-armed chromosomes based on chromosome morphology and banding characteristics. Although painting probes from the chicken (Gallus gallus, GGA) chromosomes 1–9 and Z have been widely used to investigate avian chromosome homologies, GGA microchromosome probes are rarely used in these studies because most GGA microchromosome probes generated by flow sorting often contain multiple GGA microchromosomes. In contrast, the stone curlew (Burhinus oedicnemus, BOE, Charadriiformes) has an atypical low diploid chromosome number (42) karyotype and only 4 pairs of dot-like microchromosomes; a set of chromosome-specific painting probes that cover all BOE chromosomes has been generated. To get a genome-wide view of evolutionary chromosomal rearrangements in different lineages of Ciconiiformes, we used BOE painting probes instead of GGA painting probes to analyze the karyotypes of three ciconiiform species belonging to two different families: the eastern grey heron (Ardea cinerea, ACI, 2n = 64, Ardeidae), the little egret (Egretta garzetta, EGA, 2n = 64, Ardeidae) and the crested ibis (Nipponia nippon, NNI, 2n = 68, Threskiornithidae). Results BOE painting probes display the same hybridization pattern on chromosomes of ACI and EGA, while a different hybridization pattern is observed on chromosomes of NNI. BOE autosome probes detected 21 conserved homologous segments and 5 fusions on the sixteen pairs of recognizable chromosomes of ACI and EGA, while 16 conserved homologous segments and 4 fusions were found on the twelve pairs of recognizable chromosomes of NNI. Only a portion of smaller bi-armed chromosomes in the karyotypes of the ciconiiform species could have evolved from fusions of ancestral microchromosomes. In particular BOE 5, which is the result of a fusion between two segments homologous to GGA 7 and 8 respectively, was retained also as either a single chromosome in ACI (ACI 5) and EGA (EGA 5) or had fused with a part of the BOE 10 equivalent in NNI (NNI 5). Conclusion Our painting results indicate that different chromosome rearrangements occur in different ciconiiform lineages. Some of the small-sized bi-armed chromosomes in ACI, EGA and NNI are derived from the fusions of two microchromosomes, indicating that microchromosome fusions play an important role in ciconiiform chromosome evolution. The fusion segment homologous to GGA 7 and 8 is a potential cytogenetic signature that unites Ardeidae and Threskiornithidae.
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Affiliation(s)
- Jinhuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Weiting Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Yi Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Shengbin Li
- Key Laboratory of Forensic Sciences, Ministry of Health, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, Shandong, People's Republic of China.
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China.
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Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus. BIRDS 2022. [DOI: 10.3390/birds3010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Avian sex chromosomes evolved after the divergence of birds and crocodilians from their common ancestor, so they are younger than the better-studied chromosomes of mammals. It has long been recognized that there may have been several stages to the evolution of avian sex chromosomes. For example, the CHD1 undergoes recombination in paleognaths but not neognaths. Genome assemblies have suggested that there may be variation in the timing of barriers to recombination among Neognathae, but there remains little understanding of the extent of this variability. Here, we look at partial sequences of ATP5F1A, which is on the avian Z and W chromosomes. It is known that recombination of this gene has independently ceased in Galliformes, Anseriformes, and at least five neoavian orders, but whether there are other independent cessations of recombination among Neoaves is not understood. We analyzed a combination of data extracted from published chromosomal-level genomes with data collected using PCR and cloning to identify Z and W copies in 22 orders. Our results suggest that there may be at least 19 independent cessations of recombination within Neognathae, and 3 clades that may still be undergoing recombination (or have only recently ceased recombination). Analyses of ATP5F1A protein sequences revealed an increased amino acid substitution rate for W chromosome gametologs, suggesting relaxed purifying selection on the W chromosome. Supporting this hypothesis, we found that the increased substitution rate was particularly pronounced for buried residues, which are expected to be more strongly constrained by purifying selection. This highlights the dynamic nature of avian sex chromosomes, and that this level of variation among clades means they should be a good system to understand sex chromosome evolution.
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Hallas JM, Parchman TL, Feldman CR. Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution. Mol Phylogenet Evol 2021; 167:107374. [PMID: 34896619 DOI: 10.1016/j.ympev.2021.107374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Garter snakes (Thamnophis) are a successful group of natricines endemic to North America. They have become important natural models for ecological and evolutionary research, yet prior efforts to resolve phylogenetic relationships have resulted in conflicting topologies and weak support for certain relationships. Here, we use genomic data generated with a reduced representation double-digest RADseq approach to reassess evolutionary relationships across Thamnophis. We then use the resulting phylogeny to better understand how biogeography and feeding ecology have influenced lineage diversification and morphological evolution. We recovered highly congruent and strongly supported topologies from maximum likelihood and Bayesian analyses, but some discordance with a multispecies coalescent approach. All phylogenomic estimates split Thamnophis into two clades largely defined by northern and southern North American species. Divergence time estimates and biogeographic analyses indicate a mid-Miocene origin of Thamnophis in Mexico. In addition, historic vicariant events thought to explain biogeographic patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns of diversification in Thamnophis as well. Analyses of morphological traits associated with feeding ecology showed moderate to strong phylogenetic signal. Nevertheless, phylogenetic ANOVA suggested significant differences in certain cranial morphologies between aquatic specialists and garter snakes that are terrestrial-aquatic generalists, independent of evolutionary history. Our new estimate of Thamnophis phylogeny yields an improved understanding of the biogeographic history and morphological evolution of garter snakes, and provides a robust framework for future research on these snakes.
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Affiliation(s)
- Joshua M Hallas
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA.
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
| | - Chris R Feldman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
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New Remains of Scandiavis mikkelseni Inform Avian Phylogenetic Relationships and Brain Evolution. DIVERSITY 2021. [DOI: 10.3390/d13120651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although an increasing number of studies are combining skeletal and neural morphology data in a phylogenetic context, most studies do not include extinct taxa due to the rarity of preserved endocasts. The early Eocene avifauna of the Fur Formation of Denmark presents an excellent opportunity for further study of extinct osteological and endocranial morphology as fossils are often exceptionally preserved in three dimensions. Here, we use X-ray computed tomography to present additional material of the previously described taxon Scandiavis mikkelseni and reassess its phylogenetic placement using a previously published dataset. The new specimen provides novel insights into the osteological morphology and brain anatomy of Scandiavis. The virtual endocast exhibits a morphology comparable to that of modern avian species. Endocranial evaluation shows that it was remarkably similar to that of certain extant Charadriiformes, yet also possessed a novel combination of traits. This may mean that traits previously proposed to be the result of shifts in ecology later in the evolutionary history of Charadriiformes may instead show a more complex distribution in stem Charadriiformes and/or Gruiformes depending on the interrelationships of these important clades. Evaluation of skeletal and endocranial character state changes within a previously published phylogeny confirms both S. mikkelseni and a putative extinct charadriiform, Nahmavis grandei, as charadriiform. Results bolster the likelihood that both taxa are critical fossils for divergence dating and highlight a biogeographic pattern similar to that of Gruiformes.
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Global Studies of the Host-Parasite Relationships between Ectoparasitic Mites of the Family Syringophilidae and Birds of the Order Columbiformes. Animals (Basel) 2021; 11:ani11123392. [PMID: 34944169 PMCID: PMC8697884 DOI: 10.3390/ani11123392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
The quill mites belonging to the family Syringophilidae (Acari: Prostigmata: Cheyletoidea) are obligate ectoparasites of birds. They inhabit different types of the quills, where they spend their whole life cycle. In this paper, we conducted a global study of syringophilid mites associated with columbiform birds. We examined 772 pigeon and dove individuals belonging to 112 species (35% world fauna) from all zoogeographical regions (except Madagascan) where Columbiformes occur. We measured the prevalence (IP) and the confidence interval (CI) for all infested host species. IP ranges between 4.2 and 66.7 (CI 0.2-100). We applied a bipartite analysis to determine host-parasite interaction, network indices, and host specificity on species and whole network levels. The Syringophilidae-Columbiformes network was composed of 25 mite species and 65 host species. The bipartite network was characterized by a high network level specialization H2' = 0.93, high nestedness N = 0.908, connectance C = 0.90, and high modularity Q = 0.83, with 20 modules. Moreover, we reconstructed the phylogeny of the quill mites associated with columbiform birds on the generic level. Analysis shows two distinct clades: Meitingsunes + Psittaciphilus, and Peristerophila + Terratosyringophilus.
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Montgomerie R, Hemmings N, Thompson JE, Birkhead TR. The Shapes of Birds' Eggs: Evolutionary Constraints and Adaptations. Am Nat 2021; 198:E215-E231. [PMID: 34762571 DOI: 10.1086/716928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWe studied the shapes of eggs from 955 extant bird species across the avian phylogeny, including 39 of 40 orders and 78% of 249 families. We show that the elongation component of egg shape (length relative to width) is largely the result of constraints imposed by the female's anatomy during egg formation, whereas asymmetry (pointedness) is mainly an adaptation to conditions during the incubation period. Thus, egg elongation is associated with the size of the egg in relation to both the size of the female's oviduct and her general body conformation and mode of locomotion correlated with pelvis shape. Egg asymmetry is related mainly to clutch size and the structure of the incubation site, factors that influence thermal efficiency during incubation and the risk of breakage. Importantly, general patterns across the avian phylogeny do not always reflect the trends within lower taxonomic levels. We argue that the analysis of avian egg shape is most profitably conducted within taxa where all species share similar life histories and ecologies, as there is no single factor that influences egg shape in the same way in all bird species.
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Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds. DIVERSITY 2021. [DOI: 10.3390/d13110555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
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Davis SN, Clarke JA. Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs. Evolution 2021; 76:42-57. [PMID: 34719783 DOI: 10.1111/evo.14393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/27/2022]
Abstract
Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid-consistent coloration across tissue types in all extant, nonpasserine species (n = 4022) and archelosaur outgroups in a phylogenetic framework. We collect dietary data for a subset of birds and investigate how dietary carotenoid intake may relate to carotenoid expression in various tissues. We find that carotenoid-consistent expression in skin or nonplumage keratin has a 50% probability of being present in the most recent common ancestor of Archosauria. Skin expression has a similar probability at the base of the avian crown clade, but plumage expression is unambiguously absent in that ancestor and shows hundreds of independent gains within nonpasserine neognaths, consistent with previous studies. Although our data do not support a strict sequence of tissue expression in nonpasserine birds, we find support that expression of carotenoid-consistent color in nonplumage integument structures might evolve in a correlated manner and feathers are rarely the only region of expression. Taxa with diets high in carotenoid content also show expression in more body regions and tissue types. Our results may inform targeted assays for carotenoids in tissues other than feathers, and expectations of these pigments in nonavian dinosaurs. In extinct groups, bare-skin regions and the rhamphotheca, especially in species with diets rich in plants, may express these pigments, which are not expected in feathers or feather homologues.
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Affiliation(s)
- Sarah N Davis
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712
| | - Julia A Clarke
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712.,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712
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White ND, Batz ZA, Braun EL, Braun MJ, Carleton KL, Kimball RT, Swaroop A. A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution. Mol Ecol Resour 2021; 22:587-601. [PMID: 34652059 DOI: 10.1111/1755-0998.13496] [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: 05/14/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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Affiliation(s)
- Noor D White
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA
| | - Zachary A Batz
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Karen L Carleton
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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36
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Almeida FC, Porzecanski AL, Cracraft JL, Bertelli S. The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya.
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Affiliation(s)
- Francisca C Almeida
- Instituto de Ecología, Genética y Evolución (IEGEBA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/ Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana L Porzecanski
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Joel L Cracraft
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Sara Bertelli
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
- Fundación Miguel Lillo (FML), Miguel Lillo 251, 4000 San Miguel de Tucumán, Argentina
- Unidad Ejecutora Lillo (UEL) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
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37
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Ducatez S, Field DJ. Disentangling the avian altricial-precocial spectrum: Quantitative assessment of developmental mode, phylogenetic signal, and dimensionality. Evolution 2021; 75:2717-2735. [PMID: 34608994 DOI: 10.1111/evo.14365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 01/12/2023]
Abstract
The altricial-precocial spectrum describes patterns of variation in avian developmental mode that greatly influence avian life histories. Appraising a given species' position on this spectrum is therefore fundamental to understanding patterns of avian life history evolution. However, evaluating avian developmental mode remains a relatively subjective task reliant on untested assumptions, including the notion that developmental strategies are distributed along a single dimension of statistical variation. Here, we present a quantitative multivariate framework that objectively discriminates among meaningfully different modes of avian development. We gathered information on seven hatchling and post-hatching traits for up to 4000 extant bird species, and find that most traits related to developmental mode show high phylogenetic signal and little intraclade variation, allowing unknown values to be reliably interpolated. Principal component analyses (PCAs) of these traits illustrate that most variation in hatchling state can be quantified along one dimension of trait space. However, our PCAs also reveal an important second dimension explaining variation in post-hatching behavior, enabling factors related to hatchling state and post-hatching behavior to be disentangled. In order to facilitate future macroevolutionary studies of variation in avian developmental strategies, as well as explorations of covariation between developmental mode and other aspects of avian biology, we present PC scores for 9993 extant avian species.
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Affiliation(s)
- Simon Ducatez
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Institut de Recherche pour le Développement (IRD), UMR 241 EIO (Ecosystèmes Insulaires Océaniens), Papeete, Tahiti, French Polynesia
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Museum of Zoology, University of Cambridge, Cambridge, UK
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38
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Yohe LR, Fabbri M, Hanson M, Bhullar BAS. Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change. Curr Zool 2021; 66:505-514. [PMID: 34484311 DOI: 10.1093/cz/zoaa051] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
Chemosensation is the most ubiquitous sense in animals, enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues. While there is a general conception that olfactory receptor (OR) genes evolve rapidly, the universality of this phenomenon across vertebrates, and its magnitude, are unclear. The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested. We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits. Using published genomes, we identified ORs in 21 tetrapods, including amphibians, reptiles, birds, and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes. We found that, for all clades investigated, most OR genes evolve nearly an order of magnitude faster than other protein-coding genes, with many OR genes showing signatures of diversifying selection across nearly all taxa in this study. This rapid rate of evolution suggests that chemoreceptor genes are in "evolutionary overdrive," perhaps evolving in response to the ever-changing chemical space of the environment. To obtain complementary morphological data, we stained whole fixed specimens with iodine, µCT-scanned the specimens, and digitally segmented chemosensory and nonchemosensory brain regions. We then estimated phenotypic variation within traits and among tetrapods. While we found considerable variation in chemosensory structures, they were no more diverse than nonchemosensory regions. We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space, whereas chemosensory phenotypes and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.
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Affiliation(s)
- Laurel R Yohe
- Department of Earth & Planetary Science, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - Matteo Fabbri
- Department of Earth & Planetary Science, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - Michael Hanson
- Department of Earth & Planetary Science, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - Bhart-Anjan S Bhullar
- Department of Earth & Planetary Science, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
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39
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Abstract
Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous-Paleogene (K-Pg) extinction.
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40
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Toda Y, Ko MC, Liang Q, Miller ET, Rico-Guevara A, Nakagita T, Sakakibara A, Uemura K, Sackton T, Hayakawa T, Sin SYW, Ishimaru Y, Misaka T, Oteiza P, Crall J, Edwards SV, Buttemer W, Matsumura S, Baldwin MW. Early origin of sweet perception in the songbird radiation. Science 2021; 373:226-231. [PMID: 34244416 DOI: 10.1126/science.abf6505] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.
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Affiliation(s)
- Yasuka Toda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.,Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan.,Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Qiaoyi Liang
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Eliot T Miller
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Alejandro Rico-Guevara
- Department of Biology, University of Washington, Seattle, WA 98105, USA.,Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Tomoya Nakagita
- Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ayano Sakakibara
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kana Uemura
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | | | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong.,Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Pablo Oteiza
- Flow Sensing Research Group, Max Planck Institute for Ornithology, Seewiesen Germany
| | - James Crall
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA.,Department of Entomology, University of Wisconsin-Madison, WI, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
| | - William Buttemer
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia.,School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany. .,Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
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41
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Guo XM, Wang ZF, Zhang Y, Wang RJ. Chromosomal-level assembly of the Leptodermis oblonga (Rubiaceae) genome and its phylogenetic implications. Genomics 2021; 113:3072-3082. [PMID: 34246693 DOI: 10.1016/j.ygeno.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022]
Abstract
Rubiaceae is the fourth largest and a taxonomically complex family of angiosperms. Many species in this family harbor low reproductive isolation and frequently exhibit inconsistent phenotypic characteristics. Therefore, taxonomic classification and their phylogenetic relationships in the Rubiaceae family is challenging, especially in the genus Leptodermis. Considering the low taxonomic confusion and wide distribution, Leptodermis oblonga is selected as a representative Leptodermis for genome sequencing. The assemblies resulted in 497 Mbp nuclear and 155,100 bp chloroplast genomes, respectively. Using the nuclear genome as a reference, SNPs were called from 37 Leptodermis species or varieties. The phylogenetic tree based on SNPs exhibited high resolution for species delimitation of the complex and well-resolved phylogenetic relationships in the genus. Moreover, 28,987 genes were predicted in the nuclear genome and used for comparative genomics study. As the first chromosomal-level genome of the subfamily Rubioideae in Rubiaceae, it will provide fruitfully evolutionary understanding in the family.
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Affiliation(s)
- Xiao-Ming Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Feng Wang
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China
| | - Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China.
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42
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Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
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Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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43
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Independent duplications of the Golgi phosphoprotein 3 oncogene in birds. Sci Rep 2021; 11:12483. [PMID: 34127736 PMCID: PMC8203631 DOI: 10.1038/s41598-021-91909-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Golgi phosphoprotein 3 (GOLPH3) was the first reported oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.
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44
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Burskaia V, Artyushin I, Potapova NA, Konovalov K, Bazykin GA. Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist? Genome Biol Evol 2021; 13:6284172. [PMID: 34037779 PMCID: PMC8271140 DOI: 10.1093/gbe/evab113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2021] [Indexed: 11/24/2022] Open
Abstract
In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for a genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for the detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.
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Affiliation(s)
- Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia.,Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Ilja Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nadezhda A Potapova
- Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Kirill Konovalov
- Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia.,Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
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45
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Legendre LJ, Clarke JA. Shifts in eggshell thickness are related to changes in locomotor ecology in dinosaurs. Evolution 2021; 75:1415-1430. [PMID: 33913155 DOI: 10.1111/evo.14245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 04/21/2021] [Indexed: 12/16/2022]
Abstract
Birds share an array of unique characteristics among extant land vertebrates. Among these, external and microstructural characteristics of extant bird eggs have been linked to changes in reproductive strategy that arose among non-avian theropod dinosaurs. More recently, differences in egg proportions recovered in crown birds relative to other dinosaurs were suggested as possibly linked to avian flight, but dense sampling close to its proposed origin was lacking. Here we assess the evolution of eggshell thickness in a targeted sample of 114 dinosaurs including birds, and test the relationship of eggshell thickness with potential life history correlates and locomotor mode using phylogenetic comparative methods. Only egg mass and flight are identified as significant predictors of eggshell thickness. While a high correlation between egg mass and eggshell thickness is expected, that relationship is much stronger in flying taxa, which show a significantly higher slope and lower residual variance than flightless species. This suggests stabilizing selection of eggshell thickness among theropods, as recovered for other traits in extant birds (e.g. genome size, metabolic rate). Within living birds, Eufalconimorphae present an apomorphic increase in relative eggshell thickness which remains unexplained, as few morphological synapomorphies of this clade have been identified.
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Affiliation(s)
- Lucas J Legendre
- Department of Geological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Julia A Clarke
- Department of Geological Sciences, University of Texas at Austin, Austin, TX, USA
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46
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Hanson M, Hoffman EA, Norell MA, Bhullar BAS. The early origin of a birdlike inner ear and the evolution of dinosaurian movement and vocalization. Science 2021; 372:601-609. [PMID: 33958471 DOI: 10.1126/science.abb4305] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/09/2021] [Indexed: 12/27/2022]
Abstract
Reptiles, including birds, exhibit a range of behaviorally relevant adaptations that are reflected in changes to the structure of the inner ear. These adaptations include the capacity for flight and sensitivity to high-frequency sound. We used three-dimensional morphometric analyses of a large sample of extant and extinct reptiles to investigate inner ear correlates of locomotor ability and hearing acuity. Statistical analyses revealed three vestibular morphotypes, best explained by three locomotor categories-quadrupeds, bipeds and simple fliers (including bipedal nonavialan dinosaurs), and high-maneuverability fliers. Troodontids fall with Archaeopteryx among the extant low-maneuverability fliers. Analyses of cochlear shape revealed a single instance of elongation, on the stem of Archosauria. We suggest that this transformation coincided with the origin of both high-pitched juvenile location, alarm, and hatching-synchronization calls and adult responses to them.
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Affiliation(s)
- Michael Hanson
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Eva A Hoffman
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Mark A Norell
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, USA. .,Peabody Museum of Natural History, Yale University, New Haven, CT, USA
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47
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Gousy-Leblanc M, Yannic G, Therrien JF, Lecomte N. Mapping our knowledge on birds of prey population genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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48
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Sangster G, Mayr G. Feraequornithes: a name for the clade formed by Procellariiformes, Sphenisciformes, Ciconiiformes, Suliformes and Pelecaniformes (Aves). VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e61728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent genomic data sets have resolved many aspects of higher-level phylogenetic relationships of birds. Eleven phylogenomic studies provide congruent support for a clade formed by Procellariiformes, Sphenisciformes, Ciconiiformes, Suliformes and Pelecaniformes. This clade is here named ‘Feraequornithes’ following the rules and requirements of the PhyloCode.
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Grzywacz B, Skórka P. Genome size versus geographic range size in birds. PeerJ 2021; 9:e10868. [PMID: 33614292 PMCID: PMC7881720 DOI: 10.7717/peerj.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
Why do some species occur in small, restricted areas, while others are distributed globally? Environmental heterogeneity increases with area and so does the number of species. Hence, diverse biotic and abiotic conditions across large ranges may lead to specific adaptations that are often linked to a species' genome size and chromosome number. Therefore, a positive association between genome size and geographic range is anticipated. Moreover, high cognitive ability in organisms would be favored by natural selection to cope with the dynamic conditions within large geographic ranges. Here, we tested these hypotheses in birds-the most mobile terrestrial vertebrates-and accounted for the effects of various confounding variables, such as body mass, relative brain mass, and geographic latitude. Using phylogenetic generalized least squares and phylogenetic confirmatory path analysis, we demonstrated that range size is positively associated with bird genome size but probably not with chromosome number. Moreover, relative brain mass had no effect on range size, whereas body mass had a possible weak and negative effect, and range size was larger at higher geographic latitudes. However, our models did not fully explain the overall variation in range size. Hence, natural selection may impose larger genomes in birds with larger geographic ranges, although there may be additional explanations for this phenomenon.
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Affiliation(s)
- Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Piotr Skórka
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
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Kimball RT, Hosner PA, Braun EL. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. Mol Phylogenet Evol 2021; 158:107091. [PMID: 33545275 DOI: 10.1016/j.ympev.2021.107091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
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Affiliation(s)
- Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Natural History Museum of Denmark and Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
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