1
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Cathcart CA. Multiple evolutionary pressures shape identical consonant avoidance in the world's languages. Proc Natl Acad Sci U S A 2024; 121:e2316677121. [PMID: 38917001 PMCID: PMC11228491 DOI: 10.1073/pnas.2316677121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
Languages disfavor word forms containing sequences of similar or identical consonants, due to the biomechanical and cognitive difficulties posed by patterns of this sort. However, the specific evolutionary processes responsible for this phenomenon are not fully understood. Words containing sequences of identical consonants may be more likely to arise than those without; processes of word form mutation may be more likely to remove than create sequences of identical consonants in word forms; finally, words containing identical consonants may die out more frequently than those without. Phylogenetic analyses of the evolution of homologous word forms indicate that words with identical consonants arise less frequently than those without. However, words with identical consonants do not die out more frequently than those without. Further analyses reveal that forms with identical consonants are replaced in basic meaning functions more frequently than words without. Taken together, results suggest that the underrepresentation of sequences of identical consonants is overwhelmingly a by-product of constraints on word form coinage, though processes related to word usage also serve to ensure that such patterns are infrequent in more salient vocabulary items. These findings clarify aspects of processes of lexical evolution and competition that take place during language change, optimizing communicative systems.
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Affiliation(s)
- Chundra A Cathcart
- Department of Comparative Language Science, University of Zurich, Zürich CH-8050, Switzerland
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zürich CH-8050, Switzerland
- Deutsche Forschungsgemeinschaft Center "Words, Bones, Genes, Tools", University of Tübingen, Tübingen 72074, Germany
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2
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Goloboff PA, De Laet J. Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters. Cladistics 2024; 40:209-241. [PMID: 38014464 DOI: 10.1111/cla.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/29/2023] Open
Abstract
This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states. Character-state reconstructions and evaluation of trees under the assumption of independence may easily lead to ancestral assignments that violate elementary rules of biomechanics, well-established theories relating form and function or ideas about character co-variation. An obvious example is reconstructing an ancestral bird as wingless and flying at the same time; another is reconstructing a protein-coding gene as having a stop codon in some ancestors. If the characters are optimized independently, such chimeric ancestral reconstructions can occur even when no terminal displays the impossible combination of states. A set of conventions (implemented via new TNT commands and options) allows the definition of complex rules of interaction. By recoding groups of characters with proper step-matrix costs (and excluding impossible combinations from the set of permissible states), it is possible to find the ancestral reconstructions that maximize homology (and thus the degree to which similarities can be explained by common ancestry), within the constraints imposed by the rules specified by the user. We expect that considerations of biomechanics, functional morphology and natural history will be a source of many theories on possible character dependences, and that the present implementation will encourage users to take the possibility of character dependences into account in their phylogenetic analyses.
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo, UEL (CONICET-Fundación Miguel Lillo), Miguel Lillo 251, 4000, S.M. de Tucumán, Argentina
| | - Jan De Laet
- Meise Botanic Garden, Nieuwelaan 38, Meise, Belgium
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3
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Asar Y, Sauquet H, Ho SYW. Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution. Syst Biol 2023; 72:1337-1356. [PMID: 37695237 PMCID: PMC10924723 DOI: 10.1093/sysbio/syad055] [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: 08/02/2022] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023] Open
Abstract
Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.
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Affiliation(s)
- Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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4
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Girón JC, Tarasov S, González Montaña LA, Matentzoglu N, Smith AD, Koch M, Boudinot BE, Bouchard P, Burks R, Vogt L, Yoder M, Osumi-Sutherland D, Friedrich F, Beutel RG, Mikó I. Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics. Syst Biol 2023; 72:1084-1100. [PMID: 37094905 DOI: 10.1093/sysbio/syad025] [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: 02/16/2022] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.
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Affiliation(s)
- Jennifer C Girón
- Department of Entomology, Purdue University, West Lafayette, IN, USA
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, USA
| | - Sergei Tarasov
- Finnish Museum of Natural History, University of Helsinki, Pohjoinen Rautatiekatu 13, FI-00014 Helsinki, Finland
| | | | | | - Aaron D Smith
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Markus Koch
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
| | - Brendon E Boudinot
- Department of Entomology & Nematology, University of California, Davis, One Shields Ave, CA, USA
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
| | - Patrice Bouchard
- Biodiversity and Bioresources, Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Roger Burks
- Entomology Department, University of California, Riverside, 900 University Ave. Riverside, CA, USA
| | - Lars Vogt
- TIB Leibniz Information Centre for Science and Technology, Welfengarten 1B, 30167 Hannover, Germany
| | - Matthew Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, IL, USA
| | | | - Frank Friedrich
- Institut für Zell- und Systembiologie der Tiere, Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
| | - István Mikó
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
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5
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Damian-Serrano A, Hughes M, Sutherland KR. A New Molecular Phylogeny of Salps (Tunicata: Thalicea: Salpida) and the Evolutionary History of Their Colonial Architecture. Integr Org Biol 2023; 5:obad037. [PMID: 37840689 PMCID: PMC10576244 DOI: 10.1093/iob/obad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/17/2023] Open
Abstract
Salps are marine pelagic tunicates with a complex life cycle, including a solitary and colonial stage composed of asexually budded individuals. These colonies develop into species-specific architectures with distinct zooid orientations, including transversal, oblique, linear, helical, and bipinnate chains, as well as whorls and clusters. The evolutionary history of salp colony architecture has remained obscured due to the lack of an ontology to characterize architectures, as well as a lack of phylogenetic taxon sampling and resolution of critical nodes. We (1) collected and sequenced eight species of salps that had never been sequenced before, (2) inferred the phylogenetic relationships among salps, and (3) reconstructed the evolutionary history of salp colony architecture. We collected salp specimens via offshore SCUBA diving, dissected tissue samples, extracted their DNA, amplified their 18S gene, and sequenced them using Sanger technology. We inferred the phylogeny of Salpida based on 18S using both Maximum Likelihood and Bayesian approaches. Using this phylogeny, we reconstructed the ancestral states of colony architecture using a Bayesian ordered Markov model informed by the presence and absence of specific developmental mechanisms that lead to each architecture. We find that the ancestral salp architecture is either oblique or linear, with every other state being derived. Moreover, linear chains have evolved independently at least three times. While transversal chains are developmentally basal and hypothesized to be ancestral, our phylogenetic topology and reconstructions strongly indicate that they are evolutionarily derived through the loss of zooid torsion. These traits are likely critical to multijet locomotory performance and evolving under natural selection. Our work showcases the need to study the broader diversity of salp species to gain a comprehensive understanding of their organismal biology, evolutionary history, and ecological roles in pelagic ecosystems.
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Affiliation(s)
- A Damian-Serrano
- University of Oregon, Department of Biology, Institute of Ecology and Evolution. 473 Onyx Bridge, 5289 University of Oregon, Eugene OR 97403-5289, USA
| | - M Hughes
- P.O. Box 4979, Kailua Kona HI 96745, USA
| | - K R Sutherland
- University of Oregon, Department of Biology, Institute of Ecology and Evolution. 473 Onyx Bridge, 5289 University of Oregon, Eugene OR 97403-5289, USA
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6
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Keating JN, Garwood RJ, Sansom RS. Phylogenetic congruence, conflict and consilience between molecular and morphological data. BMC Ecol Evol 2023; 23:30. [PMID: 37403037 DOI: 10.1186/s12862-023-02131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/08/2023] [Indexed: 07/06/2023] Open
Abstract
Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture.
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Affiliation(s)
- Joseph N Keating
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- Natural History Museum, London, SW7 5BD, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK.
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7
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Jiang B, He Y, Elsler A, Wang S, Keating JN, Song J, Kearns SL, Benton MJ. Extended embryo retention and viviparity in the first amniotes. Nat Ecol Evol 2023; 7:1131-1140. [PMID: 37308704 PMCID: PMC10333127 DOI: 10.1038/s41559-023-02074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/17/2023] [Indexed: 06/14/2023]
Abstract
The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles, birds and mammals. It is debated whether these fetal membranes evolved in eggs on land as an adaptation to the terrestrial environment or to control antagonistic fetal-maternal interaction in association with extended embryo retention (EER). Here we report an oviparous choristodere from the Lower Cretaceous period of northeast China. The ossification sequence of the embryo confirms that choristoderes are basal archosauromorphs. The discovery of oviparity in this assumed viviparous extinct clade, together with existing evidence, suggests that EER was the primitive reproductive mode in basal archosauromorphs. Phylogenetic comparative analyses on extant and extinct amniotes suggest that the first amniote displayed EER (including viviparity).
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Affiliation(s)
- Baoyu Jiang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China.
| | - Yiming He
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Armin Elsler
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Shengyu Wang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Joseph N Keating
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Junyi Song
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Stuart L Kearns
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Michael J Benton
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
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8
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Simões TR, Vernygora OV, de Medeiros BAS, Wright AM. Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data. Syst Biol 2023; 72:662-680. [PMID: 36773019 PMCID: PMC10276625 DOI: 10.1093/sysbio/syad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/08/2022] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].
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Affiliation(s)
- Tiago R Simões
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Oksana V Vernygora
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | | | - April M Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, USA
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9
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Tarasov S. New Phylogenetic Markov Models for Inapplicable Morphological Characters. Syst Biol 2023; 72:681-693. [PMID: 36788381 PMCID: PMC10276624 DOI: 10.1093/sysbio/syad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/15/2022] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
This article proposes new Markov models for phylogenetic inference with anatomically dependent (inapplicable) morphological characters. The proposed models can explicitly model an anatomical dependency in which one or several characters are allowed to evolve only within a specific state of the hierarchically upstream character. The new models come up in two main types depending on the type of character hierarchy. The functions for constructing custom character hierarchies are provided in the R package rphenoscate. The performance of the new models is assessed using theory and simulations. This article provides practical recommendations for using the new models in Bayesian phylogenetic inference with RevBayes. [Bayesian; inapplicable characters; likelihood; Markov models; morphology; parsimony; RevBayes.].
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Affiliation(s)
- Sergei Tarasov
- Finnish Museum of Natural History, Pohjoinen Rautatiekatu 13, FI-00014 Helsinki, Finland
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10
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Kulkarni S, Wood HM, Hormiga G. Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids). Mol Phylogenet Evol 2023:107855. [PMID: 37311493 DOI: 10.1016/j.ympev.2023.107855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (< 2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA; (currently) Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706, USA.
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA.
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11
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Liow LH, Uyeda J, Hunt G. Cross-disciplinary information for understanding macroevolution. Trends Ecol Evol 2023; 38:250-260. [PMID: 36456381 DOI: 10.1016/j.tree.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022]
Abstract
Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.
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Affiliation(s)
- Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo 0562, Norway.
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Gene Hunt
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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12
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Pohle A, Kröger B, Warnock RCM, King AH, Evans DH, Aubrechtová M, Cichowolski M, Fang X, Klug C. Early cephalopod evolution clarified through Bayesian phylogenetic inference. BMC Biol 2022; 20:88. [PMID: 35421982 PMCID: PMC9008929 DOI: 10.1186/s12915-022-01284-5] [Citation(s) in RCA: 2] [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: 06/07/2021] [Accepted: 03/22/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author's opinions on the importance of certain characters but were not based on thorough cladistic analyses. At the same time, methods of phylogenetic inference have undergone substantial improvements. For fossil datasets, which typically only include morphological data, Bayesian inference and in particular the introduction of the fossilized birth-death model have opened new possibilities. Nevertheless, many tree topologies recovered from these new methods reflect large uncertainties, which have led to discussions on how to best summarize the information contained in the posterior set of trees. RESULTS We present a large, newly compiled morphological character matrix of Cambrian and Ordovician cephalopods to conduct a comprehensive phylogenetic analysis and resolve existing controversies. Our results recover three major monophyletic groups, which correspond to the previously recognized Endoceratoidea, Multiceratoidea, and Orthoceratoidea, though comprising slightly different taxa. In addition, many Cambrian and Early Ordovician representatives of the Ellesmerocerida and Plectronocerida were recovered near the root. The Ellesmerocerida is para- and polyphyletic, with some of its members recovered among the Multiceratoidea and early Endoceratoidea. These relationships are robust against modifications of the dataset. While our trees initially seem to reflect large uncertainties, these are mainly a consequence of the way clade support is measured. We show that clade posterior probabilities and tree similarity metrics often underestimate congruence between trees, especially if wildcard taxa are involved. CONCLUSIONS Our results provide important insights into the earliest evolution of cephalopods and clarify evolutionary pathways. We provide a classification scheme that is based on a robust phylogenetic analysis. Moreover, we provide some general insights on the application of Bayesian phylogenetic inference on morphological datasets. We support earlier findings that quartet similarity metrics should be preferred over the Robinson-Foulds distance when higher-level phylogenetic relationships are of interest and propose that using a posteriori pruned maximum clade credibility trees help in assessing support for phylogenetic relationships among a set of relevant taxa, because they provide clade support values that better reflect the phylogenetic signal.
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Affiliation(s)
- Alexander Pohle
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, CH-8006, Zürich, Switzerland.
| | - Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 44, Jyrängöntie 2, FI-00014, Helsinki, Finland
| | - Rachel C M Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander Universität Erlangen-Nürnberg, Loewenichstrasse 28, 91054, Erlangen, Germany
| | - Andy H King
- Geckoella Ltd, Suite 323, 7 Bridge Street, Taunton, TA1 1TG, UK
| | - David H Evans
- Natural England, Rivers House, East Quay, Bridgwater, TA6 4YS, UK
| | - Martina Aubrechtová
- Institute of Geology and Palaeontology, Faculty of Science, Charles University, Albertov 6, 12843, Prague, Czech Republic
- Institute of Geology, Czech Academy of Sciences, Rozvojová 269, 16500, Prague, Czech Republic
| | - Marcela Cichowolski
- Instituto de Estudios Andinos "Don Pablo Groeber", CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EGA, Buenos Aires, Argentina
| | - Xiang Fang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China
| | - Christian Klug
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, CH-8006, Zürich, Switzerland
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13
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Porto DS, Dahdul WM, Lapp H, Balhoff JP, Vision TJ, Mabee PM, Uyeda J. Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies. Syst Biol 2022; 71:1290-1306. [PMID: 35285502 PMCID: PMC9558846 DOI: 10.1093/sysbio/syac022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 02/09/2022] [Accepted: 03/05/2022] [Indexed: 11/18/2022] Open
Abstract
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent “parts”, but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.]
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Affiliation(s)
- Diego S Porto
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Wasila M Dahdul
- UCI Libraries,University of California, Irvine, Irvine, CA 92623, USA
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
- Battelle, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
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14
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Baczyński J, Sauquet H, Spalik K. Exceptional evolutionary lability of flower-like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae. AMERICAN JOURNAL OF BOTANY 2022; 109:437-455. [PMID: 35112711 PMCID: PMC9310750 DOI: 10.1002/ajb2.1819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/19/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display. METHODS The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches. RESULTS Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily. CONCLUSIONS Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.
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Affiliation(s)
- Jakub Baczyński
- Institute of Evolutionary Biology, Faculty of BiologyUniversity of Warsaw Biological and Chemical Research CentreWarsawPoland
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSW2000Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
| | - Krzysztof Spalik
- Institute of Evolutionary Biology, Faculty of BiologyUniversity of Warsaw Biological and Chemical Research CentreWarsawPoland
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15
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Pates S, Wolfe JM, Lerosey-Aubril R, Daley AC, Ortega-Hernández J. New opabiniid diversifies the weirdest wonders of the euarthropod stem group. Proc Biol Sci 2022; 289:20212093. [PMID: 35135344 PMCID: PMC8826304 DOI: 10.1098/rspb.2021.2093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Once considered 'weird wonders' of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem-group euarthropods and have provided crucial data for constraining the polarity of key morphological characters in the group. Anomalocaris and its relatives (radiodonts) had worldwide distribution and survived until at least the Devonian. However, despite intense study, Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the Wheeler Formation of Utah as a new opabiniid, Utaurora comosa nov. gen. et sp. By visualizing the sample of phylogenetic topologies in treespace, our results fortify support for the position of U. comosa beyond the nodal support traditionally applied. Our phylogenetic evidence expands opabiniids to multiple Cambrian stages. Our results underscore the power of treespace visualization for resolving imperfectly preserved fossils and expanding the known diversity and spatio-temporal ranges within the euarthropod lower stem group.
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Affiliation(s)
- Stephen Pates
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Rudy Lerosey-Aubril
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Allison C Daley
- Institute of Earth Sciences, University of Lausanne, Géopolis, 1015 Lausanne, Switzerland
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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16
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Tarasov S, Mikó I, Yoder MJ. ontoFAST: An R package for interactive and semi‐automatic annotation of characters with biological ontologies. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergei Tarasov
- Finnish Museum of Natural History Helsinki Finland
- National Institute for Mathematical and Biological Synthesis University of Tennessee Knoxville TN USA
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17
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May MR, Contreras DL, Sundue MA, Nagalingum NS, Looy CV, Rothfels CJ. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity. Syst Biol 2021; 70:1232-1255. [PMID: 33760075 PMCID: PMC8513765 DOI: 10.1093/sysbio/syab020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth-death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.].
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Affiliation(s)
- Michael R May
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
| | - Dori L Contreras
- Department of Paleontology, Perot Museum of Nature and Science, 2201 N. Field Street, Dallas TX 75201, USA
| | - Michael A Sundue
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
- The Pringle Herbarium, University of Vermont, 305 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Nathalie S Nagalingum
- Department of Botany, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Cindy V Looy
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
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18
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Goloboff PA, De Laet J, Ríos-Tamayo D, Szumik CA. A reconsideration of inapplicable characters, and an approximation with step-matrix recoding. Cladistics 2021; 37:596-629. [PMID: 34570932 DOI: 10.1111/cla.12456] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Thus, the classical argument for parsimony directly links homoplasy with explanatory power. When characters are hierarchically related, a first character may represent a primary structure such as tail absence/presence and a secondary (subordinate) character may describe tail colour; this makes tail colour inapplicable when tail is absent. It has been proposed that such character hierarchies should be evaluated on the same logical basis as standard characters, maximizing the number of similarities accounted for by secondary homology, i.e. common ancestry. Previous evaluations of the homology of a given ancestral reconstruction contain the unintuitive quantity "subcharacters" (number of regions of applicability). Rather than counting subcharacters, this paper proposes an equivalent but more intuitive formulation, based on counting the number of changes into each separate state. In this formulation, x-transformations, the homoplasy for the reconstruction is simply the number of changes into the state beyond the first, summed over all states. There is thus no direct connection between homoplasy and number of steps, only between homoplasy and extra steps. The link between the two formulations is that, for any region of applicability of any character, a subcharacter can be interpreted as the change into the state that is plesiomorphic in that region. Although some authors have claimed that the equivalence between maximizing explanatory power and minimizing independent originations of similar features (i.e. the standard justification of parsimony) does not hold for inapplicable characters, evaluating homoplasy with x-transformations clearly connects the two sides of that equation. Furthermore, as the evaluation with x-transformations provides a direct count and a straightforward interpretation of homoplasy, it extends naturally into implied weighting, and sheds light on problems with additive, step-matrix or continuous characters. It also allows deriving transformation costs for recoding hierarchies as step-matrix characters (where recoded states correspond to permissible combinations of states in primary and secondary characters), so that homology of the original observations is properly measured. Those transformation costs set the cost of gaining the primary structure to the maximum difference between "present" states plus cost of loss, and difference between "present" states to the sum of user-defined transformation costs between secondary features. With such recoding, invoking multiple independent derivations of the structure and similar features will cost as many extra "steps" as the instances of similarities (in both original characters) that are not being homologized. The step-matrix recoding also can take into account nested dependences. We present a simple convention for naming characters, which TNT can use to automatically convert the original data into a step-matrix form and set the proper transformation costs. Finally, the basic elements for handling inapplicable characters in the context of maximum-likelihood inference are outlined, and some quantitative comparisons between different approaches to inapplicables are provided.
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel de Tucumán, 4000, Argentina.,American Museum of Natural of Natural History, New York, NY, USA
| | - Jan De Laet
- Göteborgs Botaniska Trädgård, Göteborg, Sweden
| | - Duniesky Ríos-Tamayo
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel de Tucumán, 4000, Argentina
| | - Claudia A Szumik
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel de Tucumán, 4000, Argentina
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19
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Knyshov A, Weirauch C, Hoey-Chamberlain R. Phylogenetic relationships and revised classification of the true bug infraorder Dipsocoromorpha (Insecta: Hemiptera: Heteroptera). Cladistics 2021; 37:248-275. [PMID: 34478197 DOI: 10.1111/cla.12435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
Currently comprising only about 430 species, Dipsocoromorpha or minute litter bugs are one of the small infraorders of Heteroptera. They are classified into five morphologically distinct families--Ceratocombidae, Dipsocoridae, Hypsipterygidae, Schizopteridae and Stemmocryptidae--but relationships among and within these families are poorly understood owing to the lack of phylogenetic studies. A phylogenetic hypothesis based on combined molecular and morphological data is important to both evaluate and revise the higher-level classification and to explore the evolutionary history of morphological features including elytriform (or beetle-like) forewings, that seem to have evolved multiple times in this group, jumping devices, and the highly modified and diverse male genitalia. We here use a dataset combining Sanger-derived (~4500 bp; 108 taxa) and Illumina-generated (~7500 bp; 24 taxa) sequence data with a morphological matrix (159 characters) and taxon sampling that comprises all currently recognized family-, subfamily- and tribal-level taxa and comprehensive genus-level sampling to investigate phylogenetic relationships within litter bugs. Our results support the monophyly of Dipsocoromorpha, Schizopteridae and Dipsocoridae, whereas Ceratocombidae and the schizopterine subfamily "Ogeriinae" are polyphyletic and paraphyletic, respectively. A new classification is proposed that recognizes six families, including Trichotonannidae, stat.n., and two subfamilies each within the two larger families Ceratocombidae and Schizopteridae. Ancestral state reconstructions outline the complex evolutionary history of many morphological characters, including 15 independent origins of elytriform forewings, and at least five shifts in the degree of genitalic asymmetry.
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Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christiane Weirauch
- Department of Entomology, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Rochelle Hoey-Chamberlain
- Department of Entomology, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
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20
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Kallal RJ, Kulkarni SS, Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Hormiga G. Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics 2021; 37:298-316. [PMID: 34478199 DOI: 10.1111/cla.12439] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs-perhaps their most emblematic attribute-is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira-Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree-of-life. Overall, we provide the most comprehensive spider tree-of-life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Siddharth S Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, Bergen, 5020, Norway
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Miquel A Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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21
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Abstract
Cleistogamous flowers never fully bloom and are thought to have evolved as a means to promote self-fertilisation. A new study reveals that this curious feature arose more frequently in flowers with bilateral symmetry.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia; Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.
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22
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Porto DS, Almeida EAB, Pennell MW. Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees. Syst Biol 2021; 70:295-306. [PMID: 32722788 PMCID: PMC7882150 DOI: 10.1093/sysbio/syaa059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022] Open
Abstract
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is a useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. [Apidae; entropy; morphological modules; phenotypic integration; phylogenetic information.].
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Affiliation(s)
- Diego S Porto
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061 USA
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
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Hopkins MJ, St John K. Incorporating Hierarchical Characters into Phylogenetic Analysis. Syst Biol 2021; 70:1163-1180. [PMID: 33560427 DOI: 10.1093/sysbio/syab005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/28/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where interval nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the affects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch's algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters.
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Affiliation(s)
- Melanie J Hopkins
- Division of Paleontology (Invertebrates), American Museum of Natural History, New York, NY, USA
| | - Katherine St John
- Department of Computer Science, Hunter College, City University of New York, New York, NY, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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Abstract
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
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Affiliation(s)
- Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, 5020 Bergen, Norway;
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA;
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25
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Boyko JD, Beaulieu JM. Generalized hidden Markov models for phylogenetic comparative datasets. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13534] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- James D. Boyko
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Jeremy M. Beaulieu
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
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26
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Smith SD, Pennell MW, Dunn CW, Edwards SV. Phylogenetics is the New Genetics (for Most of Biodiversity). Trends Ecol Evol 2020; 35:415-425. [DOI: 10.1016/j.tree.2020.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
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Tarasov S. The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks. Syst Biol 2020; 69:392-400. [PMID: 31372653 DOI: 10.1093/sysbio/syz050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
What constitutes a discrete morphological character versus character state has been long discussed in the systematics literature but the consensus on this issue is still missing. Different methods of classifying organismal features into characters and character states (CCSs) can dramatically affect the results of phylogenetic analyses. Here, I show that, in the framework of Markov models, the modular structure of the gene regulatory network (GRN) underlying trait development, and the hierarchical nature of GRN evolution, essentially remove the distinction between morphological CCS, thus endowing the CCS with an invariant property with respect to each other. This property allows the states of one character to be represented as several individual characters and vice versa. In practice, this means that a phenotype can be encoded using a set of characters or just one complex character with numerous states. The representation of a phenotype using one complex character can be implemented in Markov models of trait evolution by properly structuring transition rate matrix.
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Affiliation(s)
- Sergei Tarasov
- Finnish Museum of Natural History, Pohjoinen Rautatiekatu 13, FI-00014 Helsinki, Finland.,Department of Biological Sciences, Virginia Tech, 4076 Derring Hall, 926 West Campus Drive, Blacksburg, VA 24061, USA.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996, USA
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Abstract
ABSTRACT
How much evolutionary change in development do we expect? In this Spotlight, we argue that, as developmental biologists, we are in a prime position to contribute to the definition of a null hypothesis for developmental evolution: in other words, a hypothesis for how much developmental evolution we expect to observe over time. Today, we have access to an unprecedented array of developmental data from across the tree of life. Using these data, we can now consider development in the light of evolution, and vice versa, more deeply than ever before. As we do this, we may need to re-examine previous assumptions that appeared to serve us well when data points were fewer. Specifically, we think it is important to challenge assumptions that change is very rare for all developmental traits, especially if this assumption is used to sustain an erroneous view that evolution always optimizes adaptive traits toward increasing complexity.
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Affiliation(s)
- Samuel H. Church
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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29
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Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Syst Biol 2020; 69:345-362. [PMID: 31596473 PMCID: PMC7672696 DOI: 10.1093/sysbio/syz067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023] Open
Abstract
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.].
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Affiliation(s)
- Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Wasila M Dahdul
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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31
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Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE. Interaction among ploidy, breeding system and lineage diversification. THE NEW PHYTOLOGIST 2019; 224:1252-1265. [PMID: 31617595 DOI: 10.1111/nph.16184] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/14/2019] [Indexed: 05/28/2023]
Abstract
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
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Affiliation(s)
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - William A Freyman
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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Wright AM. A Systematist's Guide to Estimating Bayesian Phylogenies From Morphological Data. INSECT SYSTEMATICS AND DIVERSITY 2019; 3:2. [PMID: 31355348 PMCID: PMC6643758 DOI: 10.1093/isd/ixz006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Indexed: 05/07/2023]
Abstract
Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists. This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.
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Affiliation(s)
- April M Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA
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