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Lian L, Peng HW, Erst AS, Ortiz RDC, Jabbour F, Chen ZD, Wang W. Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters. Cladistics 2024. [PMID: 38469932 DOI: 10.1111/cla.12573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.
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Affiliation(s)
- Lian Lian
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia
| | - Rosa Del C Ortiz
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, Missouri, 63110, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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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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3
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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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4
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Jasinski SE, Sullivan RM, Carter AM, Johnson EH, Dalman SG, Zariwala J, Currie PJ. Osteology and reassessment of Dineobellator notohesperus, a southern eudromaeosaur (Theropoda: Dromaeosauridae: Eudromaeosauria) from the latest Cretaceous of New Mexico. Anat Rec (Hoboken) 2023; 306:1712-1756. [PMID: 36342817 DOI: 10.1002/ar.25103] [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: 04/01/2022] [Revised: 09/11/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Dromaeosaurids (Theropoda: Dromaeosauridae), a group of dynamic, swift predators, have a sparse fossil record, particularly at the end of the Cretaceous Period. The recently described Dineobellator notohesperus, consisting of a partial skeleton from the Upper Cretaceous (Maastrichtian) of New Mexico, is the only diagnostic dromaeosaurid to be recovered from the latest Cretaceous of the southwestern United States. Reinterpreted and newly described material include several caudal vertebrae, portions of the right radius and pubis, and an additional ungual, tentatively inferred to be from manual digit III. Unique features, particularly those of the humerus, unguals, and caudal vertebrae, distinguish D. notohesperus from other known dromaeosaurids. This material indicates different physical attributes among dromaeosaurids, such as use of the forearms, strength in the hands and feet, and mobility of the tail. Several bones in the holotype exhibit abnormal growth and are inferred to be pathologic features resulting from an injury or disease. Similar lengths of the humerus imply Dineobellator and Deinonychus were of similar size, at least regarding length and/or height, although the more gracile nature of the humerus implies Dineobellator was a more lightly built predator. A new phylogenetic analysis recovers D. notohesperus as a dromaeosaurid outside other previously known and named clades. Theropod composition of the Naashoibito Member theropod fauna is like those found in the more northern Late Cretaceous North American ecosystems. Differences in tooth morphologies among recovered theropod teeth from the Naashoibito Member also implies D. notohesperus was not the only dromaeosaurid present in its environment.
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Affiliation(s)
- Steven E Jasinski
- Department of Environmental Science and Sustainability, Harrisburg University, Harrisburg, Pennsylvania, USA
- Don Sundquist Center of Excellence in Paleontology, Johnson City, Tennessee, USA
| | - Robert M Sullivan
- New Mexico Museum of Natural History and Science, Albuquerque, New Mexico, USA
| | - Aja M Carter
- Penn Engineering - GRASP Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erynn H Johnson
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
- Paleontological Research Institution, Ithaca, New York, USA
| | - Sebastian G Dalman
- New Mexico Museum of Natural History and Science, Albuquerque, New Mexico, USA
| | - Juned Zariwala
- Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Philip J Currie
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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5
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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6
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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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7
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Sauquet H, Ramírez-Barahona S, Magallón S. What is the age of flowering plants? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3840-3853. [PMID: 35438718 DOI: 10.1093/jxb/erac130] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140-270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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8
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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9
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Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction. PLoS Biol 2021; 19:e3001414. [PMID: 34648487 PMCID: PMC8516226 DOI: 10.1371/journal.pbio.3001414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees. The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs and long-term physiographic changes. This phylogenetic natural history study offers new insights into the evolution of snake ecological diversity after the end-Cretaceous mass extinction, as they took advantage of these new opportunities.
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10
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Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nat Commun 2021; 12:5335. [PMID: 34521829 PMCID: PMC8440539 DOI: 10.1038/s41467-021-25136-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 07/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas.
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11
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Wu Y, Yan Y, Zhao Y, Gu L, Wang S, Johnson DH. Genomic bases underlying the adaptive radiation of core landbirds. BMC Ecol Evol 2021; 21:162. [PMID: 34454438 PMCID: PMC8403425 DOI: 10.1186/s12862-021-01888-5] [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: 08/28/2020] [Accepted: 08/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Core landbirds undergo adaptive radiation with different ecological niches, but the genomic bases that underlie their ecological diversification remain unclear. RESULTS Here we used the genome-wide target enrichment sequencing of the genes related to vision, hearing, language, temperature sensation, beak shape, taste transduction, and carbohydrate, protein and fat digestion and absorption to examine the genomic bases underlying their ecological diversification. Our comparative molecular phyloecological analyses show that different core landbirds present adaptive enhancement in different aspects, and two general patterns emerge. First, all three raptorial birds (Accipitriformes, Strigiformes, and Falconiformes) show a convergent adaptive enhancement for fat digestion and absorption, while non-raptorial birds tend to exhibit a promoted capability for protein and carbohydrate digestion and absorption. Using this as a molecular marker, our results show relatively strong support for the raptorial lifestyle of the common ancestor of core landbirds, consequently suggesting a single origin of raptors, followed by two secondary losses of raptorial lifestyle within core landbirds. In addition to the dietary niche, we find at temporal niche that diurnal birds tend to exhibit an adaptive enhancement in bright-light vision, while nocturnal birds show an increased adaption in dim-light vision, in line with previous findings. CONCLUSIONS Our molecular phyloecological study reveals the genome-wide adaptive differentiations underlying the ecological diversification of core landbirds.
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Affiliation(s)
- Yonghua Wu
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China.
| | - Yi Yan
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Yuanqin Zhao
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Li Gu
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Songbo Wang
- Bio-Intelligence Co. Ltd, Shenzhen, 518000, China
| | - David H Johnson
- Global Owl Project, 6504 Carriage Drive, Alexandria, VA, 22310, USA.
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12
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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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13
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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: 56] [Impact Index Per Article: 18.7] [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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14
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Degrange FJ, Pol D, Puerta P, Wilf P. Unexpected larger distribution of paleogene stem-rollers (AVES, CORACII): new evidence from the Eocene of Patagonia, Argentina. Sci Rep 2021; 11:1363. [PMID: 33446824 PMCID: PMC7809110 DOI: 10.1038/s41598-020-80479-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022] Open
Abstract
Here we present the first record of a stem-Coracii outside the Holarctic region, found in the early Eocene of Patagonia at the Laguna del Hunco locality. Ueekenkcoracias tambussiae gen. et sp. nov. consists of an incomplete right hind limb that presents the following combination of characters, characteristic of Coracii: relatively short and stout tibiotarsus, poorly developed crista cnemialis cranialis, short and wide tarsometatarsus, with the tuberositas m. tibialis cranialis located medially on the shaft, and curved and stout ungual phalanges. Although the presence of a rounded and conspicuous foramen vasculare distale and the trochlea metatarsi II strongly deflected medially resemble Primobucconidae, a fossil group only found in the Eocene of Europe and North America, our phylogenetic analysis indicates the new taxon is the basalmost known Coracii. The unexpected presence of a stem-Coracii in the Eocene of South America indicates that this clade had a more widespread distribution than previously hypothesized, already extending into the Southern Hemisphere by the early Eocene. Ueekenkcoracias tambussiae represents new evidence of the increasing diversity of stem lineages of birds in the Eocene. The new material provides novel morphological data for understanding the evolutionary origin and radiation of rollers and important data for estimates of the divergence time of the group.
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Affiliation(s)
- Federico J Degrange
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), UNC, CONICET, Avenida Vélez Sársfield 1611, X5016GCA, Córdoba, Argentina.
| | - Diego Pol
- Museo Paleontológico Egidio Feruglio-CONICET, Av. Fontana 140, U9100GYO, Trelew, Chubut, Argentina
| | - Pablo Puerta
- Museo Paleontológico Egidio Feruglio-CONICET, Av. Fontana 140, U9100GYO, Trelew, Chubut, Argentina
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA, 16802, USA
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15
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Scanes CG. Avian Physiology: Are Birds Simply Feathered Mammals? Front Physiol 2020; 11:542466. [PMID: 33240094 PMCID: PMC7680802 DOI: 10.3389/fphys.2020.542466] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/09/2020] [Indexed: 11/13/2022] Open
Abstract
There are marked differences between the physiology of birds and mammals. These reflect the evolutionary distance between the two classes with the last common ancestor estimated as existing 318 million years ago. There are analogous organ systems in birds and mammals. However, marked differences exist. For instance, in the avian gastro-intestinal tract, there is a crop at the lower end of the esophagus. This functions both to store feed and for microbial action. The avian immune system lacks lymph nodes and has a distinct organ producing B-lymphocytes, namely the bursa Fabricius. The important of spleen has been largely dismissed until recently. However, its importance in both innate and specific immunity is increasingly recognized. There is a major difference between birds and mammals is the female reproductive system as birds produce large yolk filled eggs. The precursors of the yolk are synthesized by the liver. Another difference is that there is a single ovary and oviduct in birds.
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Affiliation(s)
- Colin G. Scanes
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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16
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Scarpetta SG. Effects of phylogenetic uncertainty on fossil identification illustrated by a new and enigmatic Eocene iguanian. Sci Rep 2020; 10:15734. [PMID: 32978416 PMCID: PMC7519069 DOI: 10.1038/s41598-020-72509-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
Fossil identifications made in a phylogenetic framework are beholden to specific tree hypotheses. Without phylogenetic consensus, the systematic provenance of any given fossil can be volatile. Paleobiogeographic and divergence time hypotheses are contingent on the accurate systematic placement of fossils. Thus, fossil diagnoses should consider multiple topologies when phylogenetic resolution or clear apomorphies are lacking. However, such analyses are infrequently performed. Pleurodonta (Squamata: Iguania) is an ancient and frequently-studied lizard clade for which phylogenetic resolution is notoriously elusive. I describe a skull fossil of a new pleurodontan lizard taxon from the Eocene deposits of the Willwood Formation, Wyoming, and use the new taxon as a case-study to explore the effects of phylogenetic uncertainty on fossil identification. The relationships of the new taxon differ considerably among analyses, and resulting interpretations are correspondingly disparate. These results illustrate generalizable and severe issues with fossil interpretations made without consideration of alternative phylogenetic hypotheses.
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Affiliation(s)
- Simon G Scarpetta
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA.
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17
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Tokita M, Matsushita H, Asakura Y. Developmental mechanisms underlying webbed foot morphological diversity in waterbirds. Sci Rep 2020; 10:8028. [PMID: 32415088 PMCID: PMC7229147 DOI: 10.1038/s41598-020-64786-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/20/2020] [Indexed: 11/20/2022] Open
Abstract
The webbed feet of waterbirds are morphologically diverse and classified into four types: the palmate foot, semipalmate foot, totipalmate foot, and lobate foot. To understand the developmental mechanisms underlying this morphological diversity, we conducted a series of comparative analyses. Ancestral state reconstruction based on phylogeny assumed that the lobate feet possessed by the common coot and little grebe arose independently, perhaps through distinct developmental mechanisms. Gremlin1, which encodes a bone morphogenetic protein (BMP) antagonist and inhibits interdigital cell death (ICD) in the foot plate of avian embryos, remained expressed in the interdigital tissues of webbed feet in the duck, common coot, little grebe, and great cormorant. Differences in Gremlin1 expression pattern and proliferating cell distribution pattern in the toe tissues of the common coot and little grebe support the convergent evolution of lobate feet. In the totipalmate-footed great cormorant, Gremlin1 was expressed in all interdigital tissues at St. 31, but its expression disappeared except along the toes by St. 33. The webbing of the cormorant's totipalmate foot and duck's palmate foot may have risen from distinct developmental mechanisms.
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Affiliation(s)
- Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
| | - Hiroya Matsushita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
- Department of Polar Science, SOKENDAI (The Graduate University for Advanced Studies), 10-3 Midori-machi, Tachikawa, Tokyo, 190-8518, Japan
| | - Yuya Asakura
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui, 910-1195, Japan
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18
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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.
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19
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Field DJ, Benito J, Chen A, Jagt JWM, Ksepka DT. Late Cretaceous neornithine from Europe illuminates the origins of crown birds. Nature 2020; 579:397-401. [PMID: 32188952 DOI: 10.1038/s41586-020-2096-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/04/2020] [Indexed: 11/09/2022]
Abstract
Our understanding of the earliest stages of crown bird evolution is hindered by an exceedingly sparse avian fossil record from the Mesozoic era. The most ancient phylogenetic divergences among crown birds are known to have occurred in the Cretaceous period1-3, but stem-lineage representatives of the deepest subclades of crown birds-Palaeognathae (ostriches and kin), Galloanserae (landfowl and waterfowl) and Neoaves (all other extant birds)-are unknown from the Mesozoic era. As a result, key questions related to the ecology4,5, biogeography3,6,7 and divergence times1,8-10 of ancestral crown birds remain unanswered. Here we report a new Mesozoic fossil that occupies a position close to the last common ancestor of Galloanserae and fills a key phylogenetic gap in the early evolutionary history of crown birds10,11. Asteriornis maastrichtensis, gen. et sp. nov., from the Maastrichtian age of Belgium (66.8-66.7 million years ago), is represented by a nearly complete, three-dimensionally preserved skull and associated postcranial elements. The fossil represents one of the only well-supported crown birds from the Mesozoic era12, and is the first Mesozoic crown bird with well-represented cranial remains. Asteriornis maastrichtensis exhibits a previously undocumented combination of galliform (landfowl)-like and anseriform (waterfowl)-like features, and its presence alongside a previously reported Ichthyornis-like taxon from the same locality13 provides direct evidence of the co-occurrence of crown birds and avialan stem birds. Its occurrence in the Northern Hemisphere challenges biogeographical hypotheses of a Gondwanan origin of crown birds3, and its relatively small size and possible littoral ecology may corroborate proposed ecological filters4,5,9 that influenced the persistence of crown birds through the end-Cretaceous mass extinction.
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Affiliation(s)
- Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.
| | - Juan Benito
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, UK
| | - Albert Chen
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, UK
| | - John W M Jagt
- Natuurhistorisch Museum Maastricht, Maastricht, The Netherlands
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20
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Stroud JT, Losos JB. Bridging the Process-Pattern Divide to Understand the Origins and Early Stages of Adaptive Radiation: A Review of Approaches With Insights From Studies of Anolis Lizards. J Hered 2019; 111:33-42. [DOI: 10.1093/jhered/esz055] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractUnderstanding the origins and early stages of diversification is one of the most elusive tasks in adaptive radiation research. Classical approaches, which aim to infer past processes from present-day patterns of biological diversity, are fraught with difficulties and assumptions. An alternative approach has been to study young clades of relatively few species, which may represent the putative early stages of adaptive radiation. However, it is difficult to predict whether those groups will ever reach the ecological and morphological disparity observed in the sorts of clades usually referred to as adaptive radiations, thereby making their utility in informing the early stages of such radiations uncertain. Caribbean Anolis lizards are a textbook example of an adaptive radiation; anoles have diversified independently on each of the 4 islands in the Greater Antilles, producing replicated radiations of phenotypically diverse species. However, the underlying processes that drove these radiations occurred 30–65 million years ago and so are unobservable, rendering major questions about how these radiations came to be difficult to tackle. What did the ancestral species of the anole radiation look like? How did new species arise? What processes drove adaptive diversification? Here, we review what we have learned about the cryptic early stages of adaptive radiation from studies of Anolis lizards, and how these studies have attempted to bridge the process-pattern divide of adaptive radiation research. Despite decades of research, however, fundamental questions linking eco-evolutionary processes to macroevolutionary patterns in anoles remain difficult to answer.
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Affiliation(s)
- James T Stroud
- Department of Biology and Living Earth Collaborative, Washington University, St. Louis, MO
| | - Jonathan B Losos
- Department of Biology and Living Earth Collaborative, Washington University, St. Louis, MO
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21
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Cui YM, Wang W, Ferguson DK, Yang J, Wang YF. Fossil evidence reveals how plants responded to cooling during the Cretaceous-Paleogene transition. BMC PLANT BIOLOGY 2019; 19:402. [PMID: 31519148 PMCID: PMC6743113 DOI: 10.1186/s12870-019-1980-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Around the Cretaceous-Paleogene (K-Pg) boundary, an obvious global cooling occurred, which resulted in dramatic changes in terrestrial ecosystems and the evolutionary trends of numerous organisms. However, how plant lineages responded to the cooling has remained unknown until now. Between ca. 70-60 Ma Mesocyparis McIver & Basinger (Cupressaceae), an extinct conifer genus, was distributed from eastern Asia to western North America and provides an excellent opportunity to solve this riddle. RESULTS Here we report a new species, Mesocyparis sinica from the early Paleocene of Jiayin, Heilongjiang, northeastern China. By integrating lines of evidence from phylogeny and comparative morphology of Mesocyparis, we found that during ca.70-60 Ma, the size of seed cone of Mesocyparis more than doubled, probably driven by the cooling during the K-Pg transition, which might be an effective adaptation for seed dispersal by animals. More importantly, we discovered that the northern limit of this genus, as well as those of two other arboreal taxa Metasequoia Miki ex Hu et Cheng (gymnosperm) and Nordenskioldia Heer (angiosperm), migrated ca.4-5° southward in paleolatitude during this time interval. CONCLUSIONS Our results suggest that the cooling during the K-Pg transition may have been responsible for the increase in size of the seed cone of Mesocyparis and have driven the migration of plants southwards.
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Affiliation(s)
- Yi-Ming Cui
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - David K. Ferguson
- Department of Palaeontology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Jian Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu-Fei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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22
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Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.
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23
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Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up.
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24
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Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
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25
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Climatic shifts drove major contractions in avian latitudinal distributions throughout the Cenozoic. Proc Natl Acad Sci U S A 2019; 116:12895-12900. [PMID: 31182570 DOI: 10.1073/pnas.1903866116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many higher level avian clades are restricted to Earth's lower latitudes, leading to historical biogeographic reconstructions favoring a Gondwanan origin of crown birds and numerous deep subclades. However, several such "tropical-restricted" clades (TRCs) are represented by stem-lineage fossils well outside the ranges of their closest living relatives, often on northern continents. To assess the drivers of these geographic disjunctions, we combined ecological niche modeling, paleoclimate models, and the early Cenozoic fossil record to examine the influence of climatic change on avian geographic distributions over the last ∼56 million years. By modeling the distribution of suitable habitable area through time, we illustrate that most Paleogene fossil-bearing localities would have been suitable for occupancy by extant TRC representatives when their stem-lineage fossils were deposited. Potentially suitable habitat for these TRCs is inferred to have become progressively restricted toward the tropics throughout the Cenozoic, culminating in relatively narrow circumtropical distributions in the present day. Our results are consistent with coarse-scale niche conservatism at the clade level and support a scenario whereby climate change over geological timescales has largely dictated the geographic distributions of many major avian clades. The distinctive modern bias toward high avian diversity at tropical latitudes for most hierarchical taxonomic levels may therefore represent a relatively recent phenomenon, overprinting a complex biogeographic history of dramatic geographic range shifts driven by Earth's changing climate, variable persistence, and intercontinental dispersal. Earth's current climatic trajectory portends a return to a megathermal state, which may dramatically influence the geographic distributions of many range-restricted extant clades.
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26
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Voskarides K, Dweep H, Chrysostomou C. Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes. Hum Genomics 2019; 13:26. [PMID: 31174607 PMCID: PMC6555970 DOI: 10.1186/s40246-019-0210-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023] Open
Abstract
Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. The availability of animal genomes permitted comparison of gene content of genomes of 24 vertebrate species that evolved through adaptive radiation (representing high evolutionary rate) and of 20 vertebrate species that are considered as living fossils (representing a slow evolutionary rate or evolutionary stasis). Mammals, birds, reptiles, and bony fishes were included in the analysis. Pathway analysis was performed for genes found to be specific in adaptive radiation or evolutionary stasis respectively. Pathway analysis revealed that DNA repair and cellular response to DNA damage are important (false discovery rate = 8.35 × 10−5; 7.15 × 10−6, respectively) for species evolved through adaptive radiation. This was confirmed by further genetic in silico analysis (p = 5.30 × 10−3). Nucleotide excision repair and base excision repair were the most significant pathways. Additionally, the number of DNA repair genes was found to be linearly related to the genome size and the protein number (proteome) of the 44 animals analyzed (p < 1.00 × 10−4), this being compatible with Drake’s rule. This is the first study where radiated and living fossil species have been genetically compared. Evidence has been found that cancer-related genes have a special role in radiated species. Linear association of the number of DNA repair genes with the species genome size has also been revealed. These comparative genetics results can support the idea of punctuated equilibrium evolution.
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27
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Chester SGB, Williamson TE, Silcox MT, Bloch JI, Sargis EJ. Skeletal morphology of the early Paleocene plesiadapiform Torrejonia wilsoni (Euarchonta, Palaechthonidae). J Hum Evol 2019; 128:76-92. [PMID: 30825983 DOI: 10.1016/j.jhevol.2018.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 11/25/2022]
Abstract
Plesiadapiforms, like other Paleogene mammals, are known mostly from fossil teeth and jaw fragments. The several families of plesiadapiforms known from partial skeletons have all been reconstructed as arborealists, but differences in postcranial morphology among these taxa indicate a diversity of positional behaviors. Here we provide the first detailed descriptions and comparisons of a dentally associated partial skeleton (NMMNH P-54500) and of the most complete dentary with anterior teeth (NMMNH P-71598) pertaining to Torrejonia wilsoni, from the early Paleocene (late Torrejonian To3 interval zone) of the Nacimiento Formation, San Juan Basin, New Mexico, USA. NMMNH P-54500 is the oldest known partial skeleton of a plesiadapiform and the only known postcrania for the Palaechthonidae. This skeleton includes craniodental fragments with all permanent teeth fully erupted, and partial forelimbs and hind limbs with some epiphyses unfused, indicating that this individual was a nearly fully-grown subadult. Analysis of the forelimb suggests mobile shoulder and elbow joints, a habitually flexed forearm, and capacity for manual grasping. The hip joint allowed abduction and lateral rotation of the thigh and provides evidence for frequent orthograde postures on large diameter supports. Other aspects of the hind limb suggest a habitually flexed thigh and knee with no evidence for specialized leaping, and mobile ankle joints capable of high degrees of inversion and eversion. Although it is likely that some variability exists within the group, analysis of this skeleton suggests that palaechthonids are most like paromomyids among plesiadapiforms, but retain more plesiomorphic postcranial features than has been documented for the Paromomyidae. These observations are congruent with craniodental evidence supporting palaechthonids and paromomyids as closely related within the Paromomyoidea. The skeleton of T. wilsoni also demonstrates that many regions of the postcranium were already well adapted for arboreality within the first few million years of the diversification of placental mammals following the Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Stephen G B Chester
- Department of Anthropology and Archaeology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA; Department of Anthropology, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA.
| | - Thomas E Williamson
- New Mexico Museum of Natural History and Science, 1801 Mountain Road, NW, Albuquerque, NM 87104-1375, USA
| | - Mary T Silcox
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario, M1C 1A4, Canada
| | - Jonathan I Bloch
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611-7800, USA
| | - Eric J Sargis
- Department of Anthropology, Yale University, P. O. Box 208277, New Haven, CT 06520, USA; Division of Vertebrate Paleontology, Peabody Museum of Natural History, New Haven, CT 06520, USA
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28
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Ksepka DT, Grande L, Mayr G. Oldest Finch-Beaked Birds Reveal Parallel Ecological Radiations in the Earliest Evolution of Passerines. Curr Biol 2019; 29:657-663.e1. [PMID: 30744971 DOI: 10.1016/j.cub.2018.12.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 11/27/2022]
Abstract
Beak shape plays a key role in avian radiations and is one of the most intensely studied aspects of avian evolution and ecology [1-4]. Perhaps no other group is more closely associated with the study of beak shape than Passeriformes (passerines or perching birds), the most species-rich ordinal clade of modern birds. However, despite their extraordinary present-day diversity, our understanding of early passerine evolution has been hindered by their sparse fossil record [5, 6]. Here, we describe two new species of early Eocene stem passerines from the Green River Formation of the United States and the Messel Formation of Germany. These species are the oldest fossil birds to exhibit a finch-like beak and provide the earliest evidence for a diet focused on small, hard seeds in crown birds. Given that granivory is a key adaptation that allows passerines to exploit open temperate environments, it is notable that both species occurred in subtropical environments [7, 8]. Phylogenetic analyses place both species within the Psittacopedidae, an extinct Eocene clade of zygodactyl stem passeriforms that also includes the slender-beaked nectarivorous Pumiliornis, the short-beaked Psittacopes, and the thrush-beaked Morsoravis. Our results reveal that stem passerines attained a diversity of beak shapes paralleling many of the morphotypes present in extant passerine finches, thrushes, and sunbirds, more than 35 million years before these morphotypes arose in the crown group. Extinction of these ecologically diverse fossil taxa may be linked to more sophisticated nest construction in anisodactyl crown passerines versus cavity-nesting in Eocene zygodactyl stem passerines [9].
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Affiliation(s)
- Daniel T Ksepka
- Bruce Museum, Greenwich, CT 06830, USA; Field Museum of Natural History, Chicago, IL 60605, USA; American Museum of Natural History, New York, NY 10024, USA; Smithsonian Institution, Washington, DC 20013, USA.
| | - Lance Grande
- Field Museum of Natural History, Chicago, IL 60605, USA; American Museum of Natural History, New York, NY 10024, USA; University of Chicago, Chicago, IL 60637, USA
| | - Gerald Mayr
- Senckenberg Research Institute, Frankfurt am Main, Germany
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Crouch NMA, Ricklefs RE. Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds. Am Nat 2019; 193:E78-E91. [PMID: 30912971 DOI: 10.1086/701630] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.
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Sustaita D, Gloumakov Y, Tsang LR, Dollar AM. Behavioral correlates of semi-zygodactyly in Ospreys ( Pandion haliaetus) based on analysis of internet images. PeerJ 2019; 7:e6243. [PMID: 30740269 PMCID: PMC6368007 DOI: 10.7717/peerj.6243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/09/2018] [Indexed: 11/20/2022] Open
Abstract
Ospreys are renowned for their fishing abilities, which have largely been attributed to their specialized talon morphology and semi-zygodactyly-the ability to rotate the fourth toe to accompany the first toe in opposition of toes II and III. Anecdotal observations indicate that zygodactyly in Ospreys is associated with prey capture, although to our knowledge this has not been rigorously tested. As a first pass toward understanding the functional significance of semi-zygodactyly in Ospreys, we scoured the internet for images of Osprey feet in a variety of circumstances. From these we cross-tabulated the number of times each of three toe configurations (anisodactylous, zygodactylous, and an intermediate condition between these) was associated with different grasping scenarios (e.g., grasping prey or perched), contact conditions (e.g., fish, other objects, or substrate), object sizes (relative to foot size), and grasping behaviors (e.g., using one or both feet). Our analysis confirms an association between zygodactyly and grasping behavior; the odds that an osprey exhibited zygodactyly while grasping objects in flight were 5.7 times greater than whilst perched. Furthermore, the odds of zygodactyly during single-foot grasps were 4.1 times greater when pictured grasping fish compared to other objects. These results suggest a functional association between predatory behavior and zygodactyly and has implications for the selective role of predatory performance in the evolution of zygodactyly more generally.
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Affiliation(s)
- Diego Sustaita
- Department of Biological Sciences, California State University, San Marcos, San Marcos, CA, USA
| | - Yuri Gloumakov
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
| | - Leah R Tsang
- Department of Zoology, Environmental and Rural Sciences, University of New England, Armidale, NSW, Australia.,Ornithology Collection, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Aaron M Dollar
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
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Abstract
Dinosaurs were large-bodied land animals of the Mesozoic that gave rise to birds. They played a fundamental role in structuring Jurassic–Cretaceous ecosystems and had physiology, growth, and reproductive biology unlike those of extant animals. These features have made them targets of theoretical macroecology. Dinosaurs achieved substantial structural diversity, and their fossil record documents the evolutionary assembly of the avian body plan. Phylogeny-based research has allowed new insights into dinosaur macroevolution, including the adaptive landscape of their body size evolution, patterns of species diversification, and the origins of birds and bird-like traits. Nevertheless, much remains unknown due to incompleteness of the fossil record at both local and global scales. This presents major challenges at the frontier of paleobiological research regarding tests of macroecological hypotheses and the effects of dinosaur biology, ecology, and life history on their macroevolution.
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Affiliation(s)
- Roger B.J. Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, United Kingdom
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Carlsen MM, Fér T, Schmickl R, Leong-Škorničková J, Newman M, Kress WJ. Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data. Mol Phylogenet Evol 2018; 128:55-68. [DOI: 10.1016/j.ympev.2018.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/09/2023]
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Budd GE, Mann RP. History is written by the victors: The effect of the push of the past on the fossil record. Evolution 2018; 72:2276-2291. [PMID: 30257040 PMCID: PMC6282550 DOI: 10.1111/evo.13593] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/01/2018] [Indexed: 02/05/2023]
Abstract
Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, SE 752 36, Sweden
| | - Richard P Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
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Pires MM, Rankin BD, Silvestro D, Quental TB. Diversification dynamics of mammalian clades during the K-Pg mass extinction. Biol Lett 2018; 14:rsbl.2018.0458. [PMID: 30258031 DOI: 10.1098/rsbl.2018.0458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 09/05/2018] [Indexed: 11/12/2022] Open
Abstract
The Cretaceous/Palaeogene (K-Pg) episode is an iconic mass extinction, in which the diversity of numerous clades abruptly declined. However, the responses of individual clades to mass extinctions may be more idiosyncratic than previously understood. Here, we examine the diversification dynamics of the three major mammalian clades in North America across the K-Pg. Our results show that these clades responded in dramatically contrasting ways to the K-Pg event. Metatherians underwent a sudden rise in extinction rates shortly after the K-Pg, whereas declining origination rates first halted diversification and later drove the loss of diversity in multituberculates. Eutherians experienced high taxonomic turnover near the boundary, with peaks in both origination and extinction rates. These findings indicate that the effects of geological episodes on diversity are context dependent and that mass extinctions can affect the diversification of clades by independently altering the extinction regime, the origination regime or both.
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Affiliation(s)
- Mathias M Pires
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas 13083-862, Brazil .,Departamento de Ecologia, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Brian D Rankin
- University of California Museum of Paleontology (UCMP), University of California, Berkeley, CA, USA
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg and Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, São Paulo 05508-900, Brazil
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Sleep NH. Geological and Geochemical Constraints on the Origin and Evolution of Life. ASTROBIOLOGY 2018; 18:1199-1219. [PMID: 30124324 DOI: 10.1089/ast.2017.1778] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.
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Affiliation(s)
- Norman H Sleep
- Department of Geophysics, Stanford University , Stanford, California
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Field DJ, Hsiang AY. A North American stem turaco, and the complex biogeographic history of modern birds. BMC Evol Biol 2018; 18:102. [PMID: 29936914 PMCID: PMC6016133 DOI: 10.1186/s12862-018-1212-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Earth's lower latitudes boast the majority of extant avian species-level and higher-order diversity, with many deeply diverging clades restricted to vestiges of Gondwana. However, palaeontological analyses reveal that many avian crown clades with restricted extant distributions had stem group relatives in very different parts of the world. RESULTS Our phylogenetic analyses support the enigmatic fossil bird Foro panarium Olson 1992 from the early Eocene (Wasatchian) of Wyoming as a stem turaco (Neornithes: Pan-Musophagidae), a clade that is presently endemic to sub-Saharan Africa. Our analyses offer the first well-supported evidence for a stem musophagid (and therefore a useful fossil calibration for avian molecular divergence analyses), and reveal surprising new information on the early morphology and biogeography of this clade. Total-clade Musophagidae is identified as a potential participant in dispersal via the recently proposed 'North American Gateway' during the Palaeogene, and new biogeographic analyses illustrate the importance of the fossil record in revealing the complex historical biogeography of crown birds across geological timescales. CONCLUSIONS In the Palaeogene, total-clade Musophagidae was distributed well outside the range of crown Musophagidae in the present day. This observation is consistent with similar biogeographic observations for numerous other modern bird clades, illustrating shortcomings of historical biogeographic analyses that do not incorporate information from the avian fossil record.
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Affiliation(s)
- Daniel J. Field
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY UK
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
| | - Allison Y. Hsiang
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
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Field DJ, Bercovici A, Berv JS, Dunn R, Fastovsky DE, Lyson TR, Vajda V, Gauthier JA. Early Evolution of Modern Birds Structured by Global Forest Collapse at the End-Cretaceous Mass Extinction. Curr Biol 2018; 28:1825-1831.e2. [PMID: 29804807 DOI: 10.1016/j.cub.2018.04.062] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/19/2018] [Accepted: 04/18/2018] [Indexed: 10/16/2022]
Abstract
The fossil record and recent molecular phylogenies support an extraordinary early-Cenozoic radiation of crown birds (Neornithes) after the Cretaceous-Paleogene (K-Pg) mass extinction [1-3]. However, questions remain regarding the mechanisms underlying the survival of the deepest lineages within crown birds across the K-Pg boundary, particularly since this global catastrophe eliminated even the closest stem-group relatives of Neornithes [4]. Here, ancestral state reconstructions of neornithine ecology reveal a strong bias toward taxa exhibiting predominantly non-arboreal lifestyles across the K-Pg, with multiple convergent transitions toward predominantly arboreal ecologies later in the Paleocene and Eocene. By contrast, ecomorphological inferences indicate predominantly arboreal lifestyles among enantiornithines, the most diverse and widespread Mesozoic avialans [5-7]. Global paleobotanical and palynological data show that the K-Pg Chicxulub impact triggered widespread destruction of forests [8, 9]. We suggest that ecological filtering due to the temporary loss of significant plant cover across the K-Pg boundary selected against any flying dinosaurs (Avialae [10]) committed to arboreal ecologies, resulting in a predominantly non-arboreal post-extinction neornithine avifauna composed of total-clade Palaeognathae, Galloanserae, and terrestrial total-clade Neoaves that rapidly diversified into the broad range of avian ecologies familiar today. The explanation proposed here provides a unifying hypothesis for the K-Pg-associated mass extinction of arboreal stem birds, as well as for the post-K-Pg radiation of arboreal crown birds. It also provides a baseline hypothesis to be further refined pending the discovery of additional neornithine fossils from the Latest Cretaceous and earliest Paleogene.
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Affiliation(s)
- Daniel J Field
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
| | - Antoine Bercovici
- Department of Paleobiology MRC-121, National Museum of Natural History, Smithsonian Institution, 10(th) Street and Constitution Avenue NW, Washington, DC 20560-0121, USA
| | - Jacob S Berv
- Department of Ecology & Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
| | - Regan Dunn
- Integrated Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - David E Fastovsky
- Department of Geosciences, University of Rhode Island, 9 East Alumni Avenue, Kingston, RI 02881, USA
| | - Tyler R Lyson
- Department of Earth Sciences, Denver Museum of Nature and Science, 2001 Colorado Boulevard, Denver, CO 80205, USA
| | - Vivi Vajda
- Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 9, 104 05 Stockholm, Sweden
| | - Jacques A Gauthier
- Department of Geology & Geophysics, Yale University 210 Whitney Avenue, New Haven, CT 06511, USA
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Fang YT, Tuanmu MN, Hung CM. Asynchronous evolution of interdependent nest characters across the avian phylogeny. Nat Commun 2018; 9:1863. [PMID: 29760391 PMCID: PMC5951845 DOI: 10.1038/s41467-018-04265-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 04/13/2018] [Indexed: 12/01/2022] Open
Abstract
Nest building is a widespread behavior among birds that reflects their adaptation to the environment and evolutionary history. However, it remains unclear how nests evolve and how their evolution relates to the bird phylogeny. Here, by examining the evolution of three nest characters—structure, site, and attachment—across all bird families, we reveal that nest characters did not change synchronically across the avian phylogeny but had disparate evolutionary trajectories. Nest structure shows stronger phylogenetic signal than nest site, while nest attachment has little variation. Nevertheless, the three characters evolved interdependently. For example, the ability of birds to explore new nest sites might depend on the emergence of novel nest structure and/or attachment. Our results also reveal labile nest characters in passerines compared with other birds. This study provides important insights into avian nest evolution and suggests potential associations between nest diversification and the adaptive radiations that generated modern bird lineages. Nearly all bird species build nests; however, there is extensive variation in both how and where their nests are built. Here, Fang and colleagues reconstruct the evolution of nest structure, nest site and nest attachment across all extant bird families.
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Affiliation(s)
- Yi-Ting Fang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Abstract
Studies reconstructing morphological evolution have long relied on simple representations of organismal form or on limited sampling of species, hindering a comprehensive understanding of the factors shaping biological diversity. Here, we combine high-resolution 3D quantification of skull shape with dense taxonomic sampling across a major vertebrate clade, birds, to demonstrate that the avian skull is formed of multiple semi-independent regions that epitomize mosaic evolution, with cranial regions and major lineages evolving with distinct rates and modes. We further show that the evolvability of different cranial regions reflects their disparate embryonic origins. Finally, we present a hypothetical reconstruction of the ancestral bird skull using this high-resolution shape data to generate a detailed estimate of extinct forms in the absence of well-preserved three-dimensional fossils. Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families. We find that the avian cranium is highly modular, consisting of seven independently evolving anatomical regions. The face and cranial vault evolve faster than other regions, showing several bursts of rapid evolution. Other modules evolve more slowly following an early burst. Both the evolutionary rate and disparity of skull modules are associated with their developmental origin, with regions derived from the anterior mandibular-stream cranial neural crest or from multiple embryonic cell populations evolving most quickly and into a greater variety of forms. Strong integration of traits is also associated with low evolutionary rate and low disparity. Individual clades are characterized by disparate evolutionary rates among cranial regions. For example, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close relatives, Falconiformes, exhibit rapid evolution in only the rostrum. Our dense sampling of cranial shape variation demonstrates that the bird skull has evolved in a mosaic fashion reflecting the developmental origins of cranial regions, with a semi-independent tempo and mode of evolution across phenotypic modules facilitating this hyperdiverse evolutionary radiation.
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