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King B, Greenhill SJ, Reid LA, Ross M, Walworth M, Gray RD. Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages. Sci Rep 2024; 14:14967. [PMID: 38942799 PMCID: PMC11213883 DOI: 10.1038/s41598-024-65810-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/24/2024] [Indexed: 06/30/2024] Open
Abstract
The Philippines are central to understanding the expansion of the Austronesian language family from its homeland in Taiwan. It remains unknown to what extent the distribution of Malayo-Polynesian languages has been shaped by back migrations and language leveling events following the initial Out-of-Taiwan expansion. Other aspects of language history, including the effect of language switching from non-Austronesian languages, also remain poorly understood. Here we apply Bayesian phylogenetic methods to a core-vocabulary dataset of Philippine languages. Our analysis strongly supports a sister group relationship between the Sangiric and Minahasan groups of northern Sulawesi on one hand, and the rest of the Philippine languages on the other, which is incompatible with a simple North-to-South dispersal from Taiwan. We find a pervasive geographical signal in our results, suggesting a dominant role for cultural diffusion in the evolution of Philippine languages. However, we do find some support for a later migration of Gorontalo-Mongondow languages to northern Sulawesi from the Philippines. Subsequent diffusion processes between languages in Sulawesi appear to have led to conflicting data and a highly unstable phylogenetic position for Gorontalo-Mongondow. In the Philippines, language switching to Austronesian in 'Negrito' groups appears to have occurred at different time-points throughout the Philippines, and based on our analysis, there is no discernible effect of language switching on the basic vocabulary.
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Affiliation(s)
- Benedict King
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Simon J Greenhill
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Lawrence A Reid
- National Museum of the Philippines, 1000, Ermita, Manila, Metro Manila, Philippines
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Malcolm Ross
- School of Culture, History and Language, Australian National University, Canberra, 2601, Australia
| | - Mary Walworth
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
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2
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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Pugh KD. Phylogenetic analysis of Middle-Late Miocene apes. J Hum Evol 2022; 165:103140. [DOI: 10.1016/j.jhevol.2021.103140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/18/2023]
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Ballesteros JA, Santibáñez-López CE, Baker CM, Benavides LR, Cunha TJ, Gainett G, Ontano AZ, Setton EVW, Arango CP, Gavish-Regev E, Harvey MS, Wheeler WC, Hormiga G, Giribet G, Sharma PP. Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida. Mol Biol Evol 2022; 39:6522129. [PMID: 35137183 PMCID: PMC8845124 DOI: 10.1093/molbev/msac021] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biology, Western Connecticut State University, Danbury, CT, 06810, USA
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Ligia R Benavides
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Tauana J Cunha
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Claudia P Arango
- Office for Research, Griffith University, Nathan, Queensland, 4111, Australia
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western, Crawley, Western Australia, 6009, Australia; Australia
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Rücklin M, King B, Cunningham JA, Johanson Z, Marone F, Donoghue PCJ. Acanthodian dental development and the origin of gnathostome dentitions. Nat Ecol Evol 2021; 5:919-926. [PMID: 33958756 DOI: 10.1038/s41559-021-01458-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/30/2021] [Indexed: 11/09/2022]
Abstract
Chondrichthyan dentitions are conventionally interpreted to reflect the ancestral gnathostome condition but interpretations of osteichthyan dental evolution in this light have proved unsuccessful, perhaps because chondrichthyan dentitions are equally specialized, or else evolved independently. Ischnacanthid acanthodians are stem-Chondrichthyes; as phylogenetic intermediates of osteichthyans and crown-chondrichthyans, the nature of their enigmatic dentition may inform homology and the ancestral gnathostome condition. Here we show that ischnacanthid marginal dentitions were statodont, composed of multicuspidate teeth added in distally diverging rows and through proximal superpositional replacement, while their symphyseal tooth whorls are comparable to chondrichthyan and osteichthyan counterparts. Ancestral state estimation indicates the presence of oral tubercles on the jaws of the gnathostome crown-ancestor; tooth whorls or tooth rows evolved independently in placoderms, osteichthyans, ischnacanthids, other acanthodians and crown-chondrichthyans. Crown-chondrichthyan dentitions are derived relative to the gnathostome crown-ancestor, which possessed a simple dentition and lacked a permanent dental lamina, which evolved independently in Chondrichthyes and Osteichthyes.
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Affiliation(s)
- Martin Rücklin
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, UK.
| | - Benedict King
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - John A Cunningham
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, UK
| | - Zerina Johanson
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, UK.
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Marjanović D. The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates. Front Genet 2021; 12:521693. [PMID: 34054911 PMCID: PMC8149952 DOI: 10.3389/fgene.2021.521693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/22/2021] [Indexed: 01/20/2023] Open
Abstract
Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.
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Affiliation(s)
- David Marjanović
- Department of Evolutionary Morphology, Science Programme “Evolution and Geoprocesses”, Museum für Naturkunde – Leibniz Institute for Evolutionary and Biodiversity Research, Berlin, Germany
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Mongiardino Koch N, Garwood RJ, Parry LA. Fossils improve phylogenetic analyses of morphological characters. Proc Biol Sci 2021; 288:20210044. [PMID: 33947239 PMCID: PMC8246652 DOI: 10.1098/rspb.2021.0044] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.
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Affiliation(s)
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
- Earth Sciences Department, Natural History Museum, London, UK
| | - Luke A Parry
- Department of Earth Sciences, University of Oxford, Oxford, UK
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King B. Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans. Biol Lett 2019; 15:20190288. [PMID: 31311486 PMCID: PMC6684994 DOI: 10.1098/rsbl.2019.0288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022] Open
Abstract
There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the 'psarolepid' osteichthyans. The 'psarolepids', which include the earliest known osteichthyans, are weakly supported as stem osteichthyans under parsimony but strongly supported as sarcopterygians in Bayesian analysis. The Bayesian result is driven by just two characters, both of which relate to the intracranial joint of sarcopterygians. Important characters that support a stem osteichthyan affinity for 'psarolepids', such as the absence of tooth enamel, have virtually no effect in a Bayesian framework. This is because of a bias towards characters with relatively complete sampling, a bias that has previously been reported for molecular data. This has important implications for Bayesian analysis of morphological datasets in general, as characters from different body parts commonly have different levels of coding completeness. Methods to critically appraise character support for conflicting phylogenetic hypotheses, such as that used here, should form an important part of phylogenetic analyses.
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Affiliation(s)
- Benedict King
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands
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