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Pol D, Baiano MA, Černý D, Novas FE, Cerda IA, Pittman M. A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria. Cladistics 2024; 40:307-356. [PMID: 38771085 DOI: 10.1111/cla.12583] [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: 01/05/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous-Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe Koleken inakayali gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. Koleken inakayali is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from Carnotaurus sastrei (the only other abelisaurid known from the La Colonia Formation). Koleken inakayali is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian-Maastrichtian), such as Aucasaurus, Niebla and Carnotaurus. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.
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Affiliation(s)
- Diego Pol
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mattia Antonio Baiano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Área Laboratorio e Investigación, Museo Municipal Ernesto Bachmann, Villa El Chocón, Neuquén, Argentina
- Universidad Nacional de Río Negro (UNRN), General Roca, Río Negro, Argentina
| | - David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Fernando E Novas
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ignacio A Cerda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Negro (UNRN), General Roca, Río Negro, Argentina
- Instituto de Investigación en Paleobiología y Geología (IIPG), General Roca, Río Negro, Argentina
- Museo Provincial Carlos Ameghino, Cipolletti, Río Negro, Argentina
| | - Michael Pittman
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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2
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Flores JR, Bippus AC, de Ullivarri CF, Suárez GM, Hyvönen J, Tomescu AMF. Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis. THE NEW PHYTOLOGIST 2023; 240:2137-2150. [PMID: 37697646 DOI: 10.1111/nph.19254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Divergence times based on molecular clock analyses often differ from those derived from total-evidence dating (TED) approaches. For bryophytes, fossils have been excluded from previous assessments of divergence times, and thus, their utility in dating analyses remains unexplored. Here, we conduct the first TED analyses of the complex thalloid liverworts (Marchantiopsida) that include fossils and evaluate macroevolutionary trends in morphological 'diversity' (disparity) and rates. Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers (sampled from nuclear, plastid and mitochondrial genomes). Taxon sampling spanned 56 extant species - representing all the orders within Marchantiophyta and extant genera within Marchantiales - and eight fossil taxa. Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic. Morphological change rate was high early in the history of the group, but it barely increased after Late Cretaceous. Disparity-through-time analyses support a fast increase in diversity until the Middle Triassic (c. 250 Ma), after which phenotypic evolution slows down considerably. Incorporating fossils in analyses challenges previous assumptions on the affinities of extinct taxa and indicates that complex thalloid liverworts radiated c. 125 Ma earlier than previously inferred.
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Affiliation(s)
- Jorge R Flores
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Instituto de Paleontología y Sedimentología, Sección Paleobotánica, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Alexander C Bippus
- Indian Natural Resource Science and Engineering Program + Diversity in STEM, 1 Harpst St, Arcata, CA, 95521, USA
| | - Carmen Fernández de Ullivarri
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 251, T4000JFE, San Miguel de Tucumán, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) & Organismal and Evolutionary Biology & Viikki Plant Science Centre, University of Helsinki, PO Box 7, FI-00014, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University Humboldt, Arcata, CA, 95521, USA
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3
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Fleming JF, Valero‐Gracia A, Struck TH. Identifying and addressing methodological incongruence in phylogenomics: A review. Evol Appl 2023; 16:1087-1104. [PMID: 37360032 PMCID: PMC10286231 DOI: 10.1111/eva.13565] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.
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4
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Barker CT, Naish D, Gostling NJ. Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous). PeerJ 2023; 11:e15453. [PMID: 37273543 PMCID: PMC10239232 DOI: 10.7717/peerj.15453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Isolated spinosaurid teeth are relatively well represented in the Lower Cretaceous Wealden Supergroup of southern England, UK. Until recently it was assumed that these teeth were referable to Baryonyx, the type species (B. walkeri) and specimen of which is from the Barremian Upper Weald Clay Formation of Surrey. British spinosaurid teeth are known from formations that span much of the c. 25 Ma depositional history of the Wealden Supergroup, and recent works suggest that British spinosaurids were more taxonomically diverse than previously thought. On the basis of both arguments, it is appropriate to doubt the hypothesis that isolated teeth from outside the Upper Weald Clay Formation are referable to Baryonyx. Here, we use phylogenetic, discriminant and cluster analyses to test whether an isolated spinosaurid tooth (HASMG G369a, consisting of a crown and part of the root) from a non-Weald Clay Formation unit can be referred to Baryonyx. HASMG G369a was recovered from an uncertain Lower Cretaceous locality in East Sussex but is probably from a Valanginian exposure of the Hastings Group and among the oldest spinosaurid material known from the UK. Spinosaurid affinities are both quantitatively and qualitatively supported, and HASMG G369a does not associate with Baryonyx in any analysis. This supports recent reinterpretations of the diversity of spinosaurid in the Early Cretaceous of Britain, which appears to have been populated by multiple spinosaurid lineages in a manner comparable to coeval Iberian deposits. This work also reviews the British and global records of early spinosaurids (known mainly from dental specimens), and revisits evidence for post-Cenomanian spinosaurid persistence.
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Affiliation(s)
- Chris T. Barker
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - Darren Naish
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Neil J. Gostling
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, Southampton, United Kingdom
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5
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Kinateder T, Drexler L, Straub K, Merkl R, Sterner R. Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis. Protein Sci 2023; 32:e4536. [PMID: 36502290 PMCID: PMC9798254 DOI: 10.1002/pro.4536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.
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Affiliation(s)
- Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Lukas Drexler
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
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6
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Timilsena PR, Barrett CF, Piñeyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, Álvarez-Buylla ER, dePamphilis CW. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages. Genome Biol Evol 2022; 15:6965378. [PMID: 36582124 PMCID: PMC9887272 DOI: 10.1093/gbe/evac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Georgia
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 1-1, Amakubo 4, Tsukuba, 305-0005, Japan
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri–Columbia, Columbia, Missouri
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 1485
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin,Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 3060
| | - Esteban Martínez-Salas
- Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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7
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Griffin CT, Wynd BM, Munyikwa D, Broderick TJ, Zondo M, Tolan S, Langer MC, Nesbitt SJ, Taruvinga HR. Africa's oldest dinosaurs reveal early suppression of dinosaur distribution. Nature 2022; 609:313-319. [PMID: 36045297 DOI: 10.1038/s41586-022-05133-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. 12-14) had given way to highly endemic assemblages12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America4,19-21 and India19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.
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Affiliation(s)
- Christopher T Griffin
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA. .,Department of Earth and Planetary Sciences, Yale University, New Haven, CT, USA. .,Yale Peabody Museum of Natural History, Yale University, New Haven, CT, USA.
| | - Brenen M Wynd
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - Darlington Munyikwa
- National Museums and Monuments of Zimbabwe, Harare, Zimbabwe.,Department of Geology and Paleontology, Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe
| | | | - Michel Zondo
- Department of Geology and Paleontology, Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe
| | | | - Max C Langer
- Departamento de Biologia, Universidade de São Paulo, São Paulo, Brazil
| | | | - Hazel R Taruvinga
- Department of Geology and Paleontology, Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe.,School of Agriculture and Natural Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
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8
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Smith MR. Using information theory to detect rogue taxa and improve consensus trees. Syst Biol 2021; 71:1088-1094. [PMID: 34951650 PMCID: PMC9366444 DOI: 10.1093/sysbio/syab099] [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: 07/15/2021] [Revised: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022] Open
Abstract
“Rogue” taxa of uncertain affinity can confound attempts to summarize the results of phylogenetic analyses. Rogues reduce resolution and support values in consensus trees, potentially obscuring strong evidence for relationships between other taxa. Information theory provides a principled means of assessing the congruence between a set of trees and their consensus, allowing rogue taxa to be identified more effectively than when using ad hoc measures of tree quality. A basic implementation of this approach in R recovers reduced consensus trees that are better resolved, more accurate, and more informative than those generated by existing methods. [Consensus trees; information theory; phylogenetic software; Rogue taxa.]
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Affiliation(s)
- Martin R Smith
- Department of Earth Sciences, Durham University, Lower Mountjoy, Durham, DH1 3LE, UK
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9
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Barker CT, Hone DWE, Naish D, Cau A, Lockwood JAF, Foster B, Clarkin CE, Schneider P, Gostling NJ. New spinosaurids from the Wessex Formation (Early Cretaceous, UK) and the European origins of Spinosauridae. Sci Rep 2021; 11:19340. [PMID: 34588472 PMCID: PMC8481559 DOI: 10.1038/s41598-021-97870-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Spinosaurids are among the most distinctive and yet poorly-known of large-bodied theropod dinosaurs, a situation exacerbated by their mostly fragmentary fossil record and competing views regarding their palaeobiology. Here, we report two new Early Cretaceous spinosaurid specimens from the Wessex Formation (Barremian) of the Isle of Wight. Large-scale phylogenetic analyses using parsimony and Bayesian techniques recover the pair in a new clade within Baryonychinae that also includes the hypodigm of the African spinosaurid Suchomimus. Both specimens represent distinct and novel taxa, herein named Ceratosuchops inferodios gen. et sp. nov. and Riparovenator milnerae gen. et sp. nov. A palaeogeographic reconstruction suggests a European origin for Spinosauridae, with at least two dispersal events into Africa. These new finds provide welcome information on poorly sampled areas of spinosaurid anatomy, suggest that sympatry was present and potentially common in baryonychines and spinosaurids as a whole, and contribute to updated palaeobiogeographic reconstructions for the clade.
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Affiliation(s)
- Chris T Barker
- Institute for Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK.
- Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK.
| | - David W E Hone
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Darren Naish
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | | | - Jeremy A F Lockwood
- School of Environment, Geography and Geosciences, University of Portsmouth, Burnaby Road, Portsmouth, PO1 3QL, UK
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | | | - Claire E Clarkin
- Institute for Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Philipp Schneider
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
- High-Performance Vision Systems, Center for Vision, Automation and Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Neil J Gostling
- Institute for Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK.
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK.
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10
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Torres A, Goloboff PA, Catalano SA. Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology). Cladistics 2021; 38:103-125. [DOI: 10.1111/cla.12477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
| | - Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- American Museum of Natural History 200 Central Park West New York NY 10024 USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 S. M. de Tucumán Tucumán 4000 Argentina
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11
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Pereyra MO, Blotto BL, Baldo D, Chaparro JC, Ron SR, Elias-Costa AJ, Iglesias PP, Venegas PJ, C. Thomé MT, Ospina-Sarria JJ, Maciel NM, Rada M, Kolenc F, Borteiro C, Rivera-Correa M, Rojas-Runjaic FJ, Moravec J, De La Riva I, Wheeler WC, Castroviejo-Fisher S, Grant T, Haddad CF, Faivovich J. Evolution in the Genus Rhinella: A Total Evidence Phylogenetic Analysis of Neotropical True Toads (Anura: Bufonidae). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.447.1.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Martín O. Pereyra
- Martín O. Pereyra: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; and Laboratorio de Genética Evolutiva “Claudio J. Bidau,” Instituto de Biología Subtropical (IBS, CONICET), Universidad Naci
| | - Boris L. Blotto
- Boris L. Blotto: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUN
| | - Diego Baldo
- Diego Baldo: Laboratorio de Genética Evolutiva “Claudio J. Bidau,” Instituto de Biología Subtropical (IBS, CONICET), Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Juan C. Chaparro
- Juan C. Chaparro: Museo de Biodiversidad del Perú, Cusco, Perú; and Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Paraninfo Universitario, Cusco
| | - Santiago R. Ron
- Santiago R. Ron: Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito
| | - Agustín J. Elias-Costa
- Agustín J. Elias-Costa: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires
| | - Patricia P. Iglesias
- Patricia P. Iglesias: Laboratorio de Genética Evolutiva “Claudio J. Bidau”, Instituto de Biología Subtropical (IBS, CONICET), Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Pablo J. Venegas
- Pablo J. Venegas: División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima
| | - Maria Tereza C. Thomé
- Maria Tereza C. Thomé: Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Rio Claro, São Paulo
| | - Jhon Jairo Ospina-Sarria
- Jhon Jairo Ospina-Sarria: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil; and Calima, Fundación para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali
| | - Natan M. Maciel
- Natan M. Maciel: Laboratório de Herpetologia e Comportamento Animal, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Marco Rada
- Marco Rada: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo
| | - Francisco Kolenc
- Francisco Kolenc: Sección Herpetología, Museo Nacional de Historia Natural, Montevideo
| | - Claudio Borteiro
- Claudio Borteiro: Sección Herpetología, Museo Nacional de Historia Natural, Montevideo
| | - Mauricio Rivera-Correa
- Mauricio Rivera-Correa: Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín
| | - Fernando J.M. Rojas-Runjaic
- Fernando J.M. Rojas-Runjaic: Fundación La Salle de Ciencias Naturales, Museo de Historia Natural La Salle (MHNLS), Venezuela; and Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Jiří Moravec
- Jiří Moravec: Department of Zoology, National Museum, Prague, Czech Republic
| | - Ignacio De La Riva
- Ignacio de la Riva: Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid
| | - Ward C. Wheeler
- Ward C. Wheeler: Division of Invertebrate Zoology, American Museum of Natural History, New York
| | - Santiago Castroviejo-Fisher
- Santiago Castroviejo-Fisher: Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil; and Research Associate, Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Taran Grant
- Taran Grant: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo; and Research Associate, Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Célio F.B. Haddad
- Célio F.B. Haddad: Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Rio Claro, São Paulo
| | - Julián Faivovich
- Julián Faivovich: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires,
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12
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Ferrari RR, Packer L. Morphological phylogeny and review of the generic classification of Colletinae (Hymenoptera: Colletidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The bee subfamily Colletinae includes 542 species, the vast majority of which (518 spp.) belong to Colletes. The generic placement of the remaining 24 species has been controversial, resulting in several classifications being proposed. Despite several recently published molecular phylogenies of Colletinae, it remains unknown (1) what morphological synapomorphies support the recognized genera, (2) in which direction some relevant functional traits (e.g. basitibial plate) have evolved and (3) whether morphology supports the available molecular data. Herein, we provide a morphological phylogeny of Colletinae, which was constructed through parsimony analyses of 186 characters. In total, 50 ingroup species were included representing all major lineages of Colletes (29 spp.), plus all but three of the non-Colletes species of Colletinae (21 spp.). Trees were estimated through equal weights and extended implied weighting. Both provide strong support for the monophyly of Colletinae and indicate that the subfamily is defined by four unique synapomorphies. Our results also confirm recent phylogenetic hypotheses showing that Colletinae can be subdivided into two major clades: one comprising the reciprocally monophyletic Mourecotelles and Xanthocotelles; the other includes Colletes plus Hemicotelles, which are also reciprocally monophyletic. We also provide a fully illustrated key to facilitate generic identification of the Colletinae.
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Affiliation(s)
- Rafael R Ferrari
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Department of Biology,York University, Toronto, ON, Canada
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13
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Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds. Curr Biol 2020; 30:4033-4046.e8. [DOI: 10.1016/j.cub.2020.06.105] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 01/04/2023]
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14
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Goloboff PA, Morales ME. A phylogenetic C interpreter for TNT. Bioinformatics 2020; 36:3988-3995. [PMID: 32221613 DOI: 10.1093/bioinformatics/btaa214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION TNT (a widely used program for phylogenetic analysis) includes an interpreter for a scripting language, but that implementation is nonstandard and uses several conventions of its own. This article describes the implementation and basic usage of a C interpreter (with all the ISO essentials) now included in TNT. A phylogenetic library includes functions that can be used for manipulating trees and data, as well as other phylogeny-specific tasks. This greatly extends the capabilities of TNT. AVAILABILITY AND IMPLEMENTATION Versions of TNT including the C interpreter for scripts can be downloaded from http://www.lillo.org.ar/phylogeny/tnt/.
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), S. M. de Tucumán 4000, Argentina
| | - Martín E Morales
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), S. M. de Tucumán 4000, Argentina
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15
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Groh SS, Upchurch P, Barrett PM, Day JJ. The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.
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Affiliation(s)
- Sebastian S Groh
- Department of Earth Sciences, University College London, London, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Paul Upchurch
- Department of Earth Sciences, University College London, London, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Julia J Day
- Department of Genetics, Environment and Evolution, University College London, London, UK
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16
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Cidade GM, Fortier D, Hsiou AS. Taxonomic and phylogenetic review of Necrosuchus ionensis (Alligatoroidea: Caimaninae) and the early evolution and radiation of caimanines. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Alligatoroidea is the most species-rich crocodylomorph clade of the Cenozoic of South America, with nearly all species belonging to the Caimaninae clade. However, the earliest records of Caimaninae in South America, which are from the Palaeocene, are based mostly on incomplete specimens, which increases the importance of detailed taxonomic and phylogenetic studies on these taxa. This paper offers a taxonomic and phylogenetic review of Necrosuchus ionensis, a caimanine species from the Salamanca Formation of the Palaeocene of Argentina. Necrosuchus ionensis is considered a valid species, albeit with a different diagnosis from that proposed by previous authors. The phylogenetic analysis shows, for the first time, that N. ionensis belongs to the derived Caimaninae clade Jacarea. However, a better understanding of the Jacarea clade is needed, and alternative placements for N. ionensis might be considered. Nevertheless, the placement of N. ionensis as a derived caimanine raises interesting perspectives on the early evolution and radiation of caimanines, which are thoroughly discussed in this paper together with other results obtained in this study, such as the recovery of the North American caimanines Bottosaurus and Tsoabichi as a clade.
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Affiliation(s)
- Giovanne M Cidade
- Laboratório de Paleontologia, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Fortier
- Laboratório de Geociências e Paleontologia, Núcleo de História Natural, CAFS, Universidade Federal do Piauí, Floriano, Piauí, Brazil
| | - Annie S Hsiou
- Laboratório de Paleontologia, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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17
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Smith MR. Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biol Lett 2019; 15:20180632. [PMID: 30958126 PMCID: PMC6405459 DOI: 10.1098/rsbl.2018.0632] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/11/2019] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analysis aims to establish the true relationships between taxa. Different analytical methods, however, can reach different conclusions. In order to establish which approach best reconstructs true relationships, previous studies have simulated datasets from known tree topologies, and identified the method that reconstructs the generative tree most accurately. On this basis, researchers have argued that morphological datasets should be analysed by Bayesian approaches, which employ an explicit probabilistic model of evolution, rather than parsimony methods-with implied weights parsimony sometimes identified as particularly inaccurate. Accuracy alone, however, is an inadequate measure of a tree's utility: a fully unresolved tree is perfectly accurate, yet contains no phylogenetic information. The highly resolved trees recovered by implied weights parsimony in fact contain as much useful information as the more accurate, but less resolved, trees recovered by Bayesian methods. By collapsing poorly supported groups, this superior resolution can be traded for accuracy, resulting in trees as accurate as those obtained by a Bayesian approach. By contrast, equally weighted parsimony analysis produces trees that are less resolved and less accurate, leading to less reliable evolutionary conclusions.
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Affiliation(s)
- Martin R. Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
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18
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Zrzavý J, Duda P, Robovský J, Okřinová I, Pavelková Řičánková V. Phylogeny of the Caninae (Carnivora): Combining morphology, behaviour, genes and fossils. ZOOL SCR 2018. [DOI: 10.1111/zsc.12293] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jan Zrzavý
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Pavel Duda
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
- Center for Theoretical Study; Charles University and Czech Academy of Sciences; Prague Czech Republic
| | - Jan Robovský
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Isabela Okřinová
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Věra Pavelková Řičánková
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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19
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Abstract
BACKGROUND Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny. RESULTS We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled. CONCLUSIONS TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .
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Affiliation(s)
- Uyen Mai
- Computer Science and Engineering, University of California at San Diego, San Diego, 92093 CA USA
| | - Siavash Mirarab
- Electrical and Computer Engineering, University of California at San Diego, San Diego, 92093 CA USA
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20
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Denton JSS, Goolsby EW. Measuring inferential importance of taxa using taxon influence indices. Ecol Evol 2018; 8:4484-4494. [PMID: 29760889 PMCID: PMC5938459 DOI: 10.1002/ece3.3941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 11/30/2022] Open
Abstract
Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty. Quantification of taxon influence using the Bayesian approach produced clear rankings for both dataset types. Bayesian taxon rankings differed from maximum likelihood (ML)‐derived rankings from a mitogenomic dataset, and the highest ranking taxa exhibited the largest interquartile range in influence estimate, suggesting variance in the estimate must be taken into account when the ranking of taxa is the feature of interest. Application of the Bayesian taxon influence index to a recent morphological analysis of the Tully Monster (Tullimonstrum) reveals that it exhibits consistently low inferential importance across two recent treatments of the taxon with alternative character codings. These results lend support to the idea that taxon influence indices may be robust to character coding and therefore effective for morphological analyses. These results underscore a need for the development of approaches to, and application of, taxon influence analyses both for the purpose of establishing robust rankings for future inquiry and for explicitly quantifying the importance of individual taxa. Quantifying the importance of individual taxa refocuses debates in morphological studies from questions of character choice/significance and taxon sampling to explicitly analytical techniques, and guides discussion of the context of new discoveries.
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Affiliation(s)
- John S S Denton
- Department of Vertebrate Paleontology American Museum of Natural History New York NY USA
| | - Eric W Goolsby
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
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21
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Madzia D, Cau A. Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature. PeerJ 2017; 5:e3782. [PMID: 28929018 PMCID: PMC5602675 DOI: 10.7717/peerj.3782] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.
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Affiliation(s)
- Daniel Madzia
- Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland
| | - Andrea Cau
- Department of Earth, Life and Environmental Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Geological and Paleontological Museum “G. Capellini”, Bologna, Italy
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22
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Bronzati M, Rauhut OWM. Braincase redescription of Efraasia minor Huene, 1908 (Dinosauria: Sauropodomorpha) from the Late Triassic of Germany, with comments on the evolution of the sauropodomorph braincase. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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23
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Phylogenetic evaluation of Amynthas earthworms from South China reveals the initial ancestral state of spermathecae. Mol Phylogenet Evol 2017; 115:106-114. [PMID: 28765092 DOI: 10.1016/j.ympev.2017.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 07/17/2017] [Indexed: 12/25/2022]
Abstract
Our knowledge of the phylogeny of the earthworm genus Amynthas under the family Megascolecidae, which is comprised of a huge number of species, is very limited compared to the better-known and much smaller family Lumbricidae. In order to investigate the phylogenetic relationships among the species within the genus Amynthas, which is the largest genus of the Megascolecidae family, nuclear and mitochondrial DNA sequences of 77 species, including 76 in-group Amynthas species collected from South China and 1 out-group species, were analyzed. A 5402bp segments composed of whole nuclear 18S rDNA and the mitochondrial genes COI, COII, ND1, 12S, and 16S was assembled from 77 species. Maximum Likelihood and Bayesian analyses of the concatenated sequences were performed. The results revealed evolution of two geographically independent lineages, both showing the ancestral state of two pairs of spermatheca (Sp.p 7/8/9). We found the species groups described by Sims and Easton (1972) to be non-monophyletic, and the origin of the parthenogenetic species group to likely be a quadthecal ancestor. These results provide modest evidence in support of an Indochinese peninsula origin of the Chinese Amynthas species and divergence of the genus once it had spread to mainland China. The findings of this study are consistent with a divergence scenario that resulted in at least one branch spreading to the Southeast of China and another branch spreading to the Southwest of China, but further research is required to confirm this interpretation of the Amynthas phylogeny.
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Fischer V, Benson RBJ, Zverkov NG, Soul LC, Arkhangelsky MS, Lambert O, Stenshin IM, Uspensky GN, Druckenmiller PS. Plasticity and Convergence in the Evolution of Short-Necked Plesiosaurs. Curr Biol 2017; 27:1667-1676.e3. [PMID: 28552354 DOI: 10.1016/j.cub.2017.04.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/06/2017] [Accepted: 04/25/2017] [Indexed: 11/18/2022]
Abstract
Plesiosaurs were the longest-surviving group of secondarily marine tetrapods, comparable in diversity to today's cetaceans. During their long evolutionary history, which spanned the Jurassic and the Cretaceous (201 to 66 Ma), plesiosaurs repeatedly evolved long- and short-necked body plans [1, 2]. Despite this postcranial plasticity, short-necked plesiosaur clades have traditionally been regarded as being highly constrained to persistent and clearly distinct ecological niches: advanced members of Pliosauridae (ranging from the Middle Jurassic to the early Late Cretaceous) have been characterized as apex predators [2-5], whereas members of the distantly related clade Polycotylidae (middle to Late Cretaceous) were thought to have been fast-swimming piscivores [1, 5-7]. We report a new, highly unusual pliosaurid from the Early Cretaceous of Russia that shows close convergence with the cranial structure of polycotylids: Luskhan itilensis gen. et sp. nov. Using novel cladistic and ecomorphological data, we show that pliosaurids iteratively evolved polycotylid-like cranial morphologies from the Early Jurassic until the Early Cretaceous. This underscores the ecological diversity of derived pliosaurids and reveals a more complex evolutionary history than their iconic representation as gigantic apex predators of Mesozoic marine ecosystems suggests. Collectively, these data demonstrate an even higher degree of morphological plasticity and convergence in the evolution of plesiosaurs than previously thought and suggest the existence of an optimal ecomorphology for short-necked piscivorous plesiosaurs through time and across phylogeny.
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Affiliation(s)
- Valentin Fischer
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK; Department of Geology, Université de Liège, 14 Allée du 6 Août, Liège 4000, Belgium.
| | - Roger B J Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - Nikolay G Zverkov
- Lomonosov Moscow State University, Leninskie Gory 1, GSP-1, Moscow 119991, Russia; Geological Institute of the Russian Academy of Sciences, Pyzhevsky Lane 7, Moscow 119017, Russia
| | - Laura C Soul
- Department of Paleobiology, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Maxim S Arkhangelsky
- Institute of Urban Studies, Saratov State Technical University, Politekhnicheskaya Ulica 77, Saratov 410054, Russia; Geological faculty, Saratov State University, Astrakhanskaya Ulica 83, Saratov 410012, Russia
| | - Olivier Lambert
- Earth and History of Life O.D., Royal Belgian Institute of Natural Sciences, 29 Rue Vautier, Brussels 1000, Belgium
| | - Ilya M Stenshin
- I.A. Goncharov Ulyanovsk Regional Natural History Museum, Boulevard Novyi Venets 3/4, Ulyanovsk 432000, Russia
| | - Gleb N Uspensky
- Natural Science Museum, Ulyanovsk State University, Ulyanovsk 432000, Russia
| | - Patrick S Druckenmiller
- University of Alaska Museum and Department of Geosciences, University of Alaska Fairbanks, 907 Yukon Drive, Fairbanks, AK 99775, USA
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Buenaventura E, Pape T. Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae). Mol Phylogenet Evol 2017; 107:619-629. [DOI: 10.1016/j.ympev.2016.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 11/24/2022]
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27
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Fernández R, Edgecombe GD, Giribet G. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Syst Biol 2016; 65:871-89. [PMID: 27162151 PMCID: PMC4997009 DOI: 10.1093/sysbio/syw041] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/28/2016] [Indexed: 11/14/2022] Open
Abstract
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Wang HC, Susko E, Roger AJ. Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection. Mol Phylogenet Evol 2016; 105:114-125. [PMID: 27568211 DOI: 10.1016/j.ympev.2016.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 11/16/2022]
Abstract
Assessing the robustness of an inferred phylogeny is an important element of phylogenetics. This is typically done with measures of stabilities at the internal branches and the variation of the positions of the leaf nodes. The bootstrap support for branches in maximum parsimony, distance and maximum likelihood estimation, or posterior probabilities in Bayesian inference, measure the uncertainty about a branch due to the sampling of the sites from genes or sampling genes from genomes. However, these measures do not reveal how taxon sampling affects branch support and the effects of taxon sampling on the estimated phylogeny. An internal branch in a phylogenetic tree can be viewed as a split that separates the taxa into two nonempty complementary subsets. We develop several split-specific measures of stability determined from bootstrap support for quartets. These include BPtaxon_split (average bootstrap percentage [BP] for all quartets involving a taxon within a split), BPsplit (BPtaxon_split averaged over taxa), BPtaxon (BPtaxon_split averaged over splits) and RBIC-taxon (average BP over all splits after removing a taxon). We also develop a pruned-tree distance metric. Application of our measures to empirical and simulated data illustrate that existing measures of overall stability can fail to detect taxa that are the primary source of a split-specific instability. Moreover, we show that the use of many reduced sets of quartets is important in being able to detect the influence of joint sets of taxa rather than individual taxa. These new measures are valuable diagnostic tools to guide taxon sampling in phylogenetic experimental design.
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Affiliation(s)
- Huai-Chun Wang
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada.
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada; Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Canada
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29
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Duda P, Jan Zrzavý. Human population history revealed by a supertree approach. Sci Rep 2016; 6:29890. [PMID: 27431856 PMCID: PMC4949479 DOI: 10.1038/srep29890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the "matrix representation with parsimony" (MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990-2014). The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African-W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul-Oceanian, E Asian, and Beringian-American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul-Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable "wildcard taxa" (e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.
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Affiliation(s)
- Pavel Duda
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Center for Theoretical Study, Charles University and Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Zrzavý
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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30
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Goloboff PA, Catalano SA. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 2016; 32:221-238. [PMID: 34727670 DOI: 10.1111/cla.12160] [Citation(s) in RCA: 850] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 11/30/2022] Open
Abstract
Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina
| | - Santiago A Catalano
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 S.M. de Tucumán, Argentina
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31
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Godoy PL, Bronzati M, Eltink E, Marsola JCDA, Cidade GM, Langer MC, Montefeltro FC. Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance. PeerJ 2016; 4:e2075. [PMID: 27257551 PMCID: PMC4888301 DOI: 10.7717/peerj.2075] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/03/2016] [Indexed: 11/20/2022] Open
Abstract
The postcranial anatomy of Crocodyliformes has historically been neglected, as most descriptions are based solely on skulls. Yet, the significance of the postcranium in crocodyliforms evolution is reflected in the great lifestyle diversity exhibited by the group, with members ranging from terrestrial animals to semi-aquatic and fully marine forms. Recently, studies have emphasized the importance of the postcranium. Following this trend, here we present a detailed description of the postcranial elements of Pissarrachampsa sera (Mesoeucrocodylia, Baurusuchidae), from the Adamantina Formation (Bauru Group, Late Cretaceous of Brazil). The preserved elements include dorsal vertebrae, partial forelimb, pelvic girdle, and hindlimbs. Comparisons with the postcranial anatomy of baurusuchids and other crocodyliforms, together with body-size and mass estimates, lead to a better understanding of the paleobiology of Pissarrachampsa sera, including its terrestrial lifestyle and its role as a top predator. Furthermore, the complete absence of osteoderms in P. sera, a condition previously known only in marine crocodyliforms, suggests osteoderms very likely played a minor role in locomotion of baurusuchids, unlike other groups of terrestrial crocodyliforms. Finally, a phylogenetic analysis including the newly recognized postcranial features was carried out, and exploratory analyses were performed to investigate the influence of both cranial and postcranial characters in the phylogeny of Crocodyliformes. Our results suggest that crocodyliform relationships are mainly determined by cranial characters. However, this seems to be a consequence of the great number of missing entries in the data set with only postcranial characters and not of the lack of potential (or synapomorphies) for this kind of data to reflect the evolutionary history of Crocodyliformes.
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Affiliation(s)
- Pedro L. Godoy
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mario Bronzati
- Bayerische Staatssammlung für Paläontologie und Geologie, Staatlichen Naturwissenschaftlichen Sammlungen Bayerns, Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Estevan Eltink
- Laboratório de Paleontologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Júlio C. de A. Marsola
- Laboratório de Paleontologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Giovanne M. Cidade
- Laboratório de Paleontologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Max C. Langer
- Laboratório de Paleontologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Felipe C. Montefeltro
- Departamento de Biologia e Zootecnia, Universidade Estadual Paulista (UNESP), Ilha Solteira, Brazil
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32
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Buenaventura E, Whitmore D, Pape T. Molecular phylogeny of the hyperdiverse genusSarcophaga(Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa. Cladistics 2016; 33:109-133. [DOI: 10.1111/cla.12161] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Eliana Buenaventura
- Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
| | - Daniel Whitmore
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Thomas Pape
- Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
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33
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Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). Mol Biol Evol 2015; 33:1110-25. [PMID: 26715628 DOI: 10.1093/molbev/msv347] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.
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Affiliation(s)
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia
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