Macroevolutionary Patterns in the Evolutionary Radiation of Archosaurs (Tetrapoda: Diapsida)
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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Genetic Change and Rates of Cladogenesis
GENETIC CHANGE AND RATES OF CLADOGENESIS JOHN C. AVISE* AND FRANCISCO J. AYALA Depariment of Genetics, University of Californiu, Davis, California 95616 Manuscript received May 12, 1975 Revised copy received July 28, 1975 ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predic- tions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic dis- tance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. -
Lineages, Splits and Divergence Challenge Whether the Terms Anagenesis and Cladogenesis Are Necessary
Biological Journal of the Linnean Society, 2015, , – . With 2 figures. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary FELIX VAUX*, STEVEN A. TREWICK and MARY MORGAN-RICHARDS Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand Received 3 June 2015; revised 22 July 2015; accepted for publication 22 July 2015 Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. -
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography of Rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus)
City University of New York (CUNY) CUNY Academic Works Publications and Research New York City College of Technology 2016 Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) Christopher Blair CUNY New York City College of Technology Santiago Sánchez-Ramírez University of Toronto How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/ny_pubs/344 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] 1Blair, C., Sánchez-Ramírez, S., 2016. Diversity-dependent cladogenesis throughout 2 western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: 3 Crotalus and Sistrurus ). Molecular Phylogenetics and Evolution 97, 145–154. 4 https://doi.org/10.1016/j.ympev.2015.12.020. © 2016. This manuscript version is made 5 available under the CC-BY-NC-ND 4.0 license. 6 7 8 Diversity-dependent cladogenesis throughout western Mexico: evolutionary 9 biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) 10 11 12 CHRISTOPHER BLAIR1*, SANTIAGO SÁNCHEZ-RAMÍREZ2,3,4 13 14 15 1Department of Biological Sciences, New York City College of Technology, Biology PhD 16 Program, Graduate Center, The City University of New York, 300 Jay Street, Brooklyn, 17 NY 11201, USA. 18 2Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks 19 Street, Toronto, ON, M5S 3B2, Canada. 20 3Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 21 ON, M5S 2C6, Canada. 22 4Present address: Environmental Genomics Group, Max Planck Institute for 23 Evolutionary Biology, August-Thienemann-Str. -
Tooth Enamel Microstructure of Revueltosaurus
Palaeontologia Electronica palaeo-electronica.org Tooth enamel microstructure of Revueltosaurus and Krzyzanowskisaurus (Reptilia:Archosauria) from the Upper Triassic Chinle Group, USA: Implications for function, growth, and phylogeny Andrew B. Heckert and Jessica A. Miller-Camp ABSTRACT Tooth enamel microstructure can carry significant phylogenetic, ontogenetic, and functional information within amniotes. Here we provide the first descriptions of the tooth enamel microstructure of two Late Triassic taxa, the crurotarsan Revueltosaurus callenderi Hunt and the putative ornithischian Krzyzanowskisaurus hunti (Heckert), which some consider closely related. To test the hypotheses that enamel thickness corresponds to function and/or phylogeny we analyzed the enamel of each at various scales, measuring enamel thickness and examining microstructural features through- out both longitudinal and cross-sectional thickness using previously established tech- niques to facilitate comparisons. Both taxa possess thick (up to ~150 µm) enamel for their size (< 20 mm crown height). Enamel in R. callenderi ranged from ~5-152 µm across a premaxillary tooth in longitudinal section, and ~42-92 µm in a maxillary/den- tary tooth transverse section. K. hunti enamel thickness was ~18-155 µm longitudinally and ~29-75 µm transversely. Both also had well-developed basal unit layers (BUL) and weakly developed columnar microstructure. Well-developed lines of incremental growth (LIG) are present in both taxa, through which the columnar enamel grades into parallel crystallite enamel. Their enamel microstructure is therefore grossly similar to that of several ornithischian taxa, especially ankylosaurs, with which they are strongly convergent, and also compares well to rauisuchids and tyrannosaurids. The relatively unique combination of microstructural characteristics in the schmelzmuster of R. -
On the Presence of the Subnarial Foramen in Prestosuchus Chiniquensis (Pseudosuchia: Loricata) with Remarks on Its Phylogenetic Distribution
Anais da Academia Brasileira de Ciências (2016) (Annals of the Brazilian Academy of Sciences) Printed version ISSN 0001-3765 / Online version ISSN 1678-2690 http://dx.doi.org/10.1590/0001-3765201620150456 www.scielo.br/aabc On the presence of the subnarial foramen in Prestosuchus chiniquensis (Pseudosuchia: Loricata) with remarks on its phylogenetic distribution LÚCIO ROBERTO-DA-SILVA1,2, MARCO A.G. FRANÇA3, SÉRGIO F. CABREIRA3, RODRIGO T. MÜLLER1 and SÉRGIO DIAS-DA-SILVA4 ¹Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Av. Roraima, 1000, Bairro Camobi, 97105-900 Santa Maria, RS, Brasil ²Laboratório de Paleontologia, Universidade Luterana do Brasil, Av. Farroupilha, 8001, Bairro São José, 92425-900 Canoas, RS, Brasil ³Laboratório de Paleontologia e Evolução de Petrolina, Campus de Ciências Agrárias, Universidade Federal do Vale do São Francisco, Rodovia BR 407, Km12, Lote 543, 56300-000 Petrolina, PE, Brasil 4Centro de Apoio à Pesquisa da Quarta Colônia, Universidade Federal de Santa Maria, Rua Maximiliano Vizzotto, 598, 97230-000 São João do Polêsine, RS, Brasil Manuscript received on July 1, 2015; accepted for publication on April 15, 2016 ABSTRACT Many authors have discussed the subnarial foramen in Archosauriformes. Here presence among Archosauriformes, shape, and position of this structure is reported and its phylogenetic importance is investigated. Based on distribution and the phylogenetic tree, it probably arose independently in Erythrosuchus, Herrerasaurus, and Paracrocodylomorpha. In Paracrocodylomorpha the subnarial foramen is oval-shaped, placed in the middle height of the main body of the maxilla, and does not reach the height of ascending process. In basal loricatans from South America (Prestosuchus chiniquensis and Saurosuchus galilei) the subnarial foramen is ‘drop-like’ shaped, the subnarial foramen is located above the middle height of the main body of the maxilla, reaching the height of ascending process, a condition also present in Herrerasaurus ischigualastensis. -
New Insights on Prestosuchus Chiniquensis Huene
New insights on Prestosuchus chiniquensis Huene, 1942 (Pseudosuchia, Loricata) based on new specimens from the “Tree Sanga” Outcrop, Chiniqua´ Region, Rio Grande do Sul, Brazil Marcel B. Lacerda1, Bianca M. Mastrantonio1, Daniel C. Fortier2 and Cesar L. Schultz1 1 Instituto de Geocieˆncias, Laborato´rio de Paleovertebrados, Universidade Federal do Rio Grande do Sul–UFRGS, Porto Alegre, Rio Grande do Sul, Brazil 2 CHNUFPI, Campus Amı´lcar Ferreira Sobral, Universidade Federal do Piauı´, Floriano, Piauı´, Brazil ABSTRACT The ‘rauisuchians’ are a group of Triassic pseudosuchian archosaurs that displayed a near global distribution. Their problematic taxonomic resolution comes from the fact that most taxa are represented only by a few and/or mostly incomplete specimens. In the last few decades, renewed interest in early archosaur evolution has helped to clarify some of these problems, but further studies on the taxonomic and paleobiological aspects are still needed. In the present work, we describe new material attributed to the ‘rauisuchian’ taxon Prestosuchus chiniquensis, of the Dinodontosaurus Assemblage Zone, Middle Triassic (Ladinian) of the Santa Maria Supersequence of southern Brazil, based on a comparative osteologic analysis. Additionally, we present well supported evidence that these represent juvenile forms, due to differences in osteological features (i.e., a subnarial fenestra) that when compared to previously described specimens can be attributed to ontogeny and indicate variation within a single taxon of a problematic but important -
Anatomically Modern Carboniferous Harvestmen Demonstrate Early Cladogenesis and Stasis in Opiliones
ARTICLE Received 14 Feb 2011 | Accepted 27 Jul 2011 | Published 23 Aug 2011 DOI: 10.1038/ncomms1458 Anatomically modern Carboniferous harvestmen demonstrate early cladogenesis and stasis in Opiliones Russell J. Garwood1, Jason A. Dunlop2, Gonzalo Giribet3 & Mark D. Sutton1 Harvestmen, the third most-diverse arachnid order, are an ancient group found on all continental landmasses, except Antarctica. However, a terrestrial mode of life and leathery, poorly mineralized exoskeleton makes preservation unlikely, and their fossil record is limited. The few Palaeozoic species discovered to date appear surprisingly modern, but are too poorly preserved to allow unequivocal taxonomic placement. Here, we use high-resolution X-ray micro-tomography to describe two new harvestmen from the Carboniferous (~305 Myr) of France. The resulting computer models allow the first phylogenetic analysis of any Palaeozoic Opiliones, explicitly resolving both specimens as members of different extant lineages, and providing corroboration for molecular estimates of an early Palaeozoic radiation within the order. Furthermore, remarkable similarities between these fossils and extant harvestmen implies extensive morphological stasis in the order. Compared with other arachnids—and terrestrial arthropods generally—harvestmen are amongst the first groups to evolve fully modern body plans. 1 Department of Earth Science and Engineering, Imperial College, London SW7 2AZ, UK. 2 Museum für Naturkunde at the Humboldt University Berlin, D-10115 Berlin, Germany. 3 Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA. Correspondence and requests for materials should be addressed to R.J.G. (email: [email protected]) and for phylogenetic analysis, G.G. (email: [email protected]). -
Physical and Environmental Drivers of Paleozoic Tetrapod Dispersal Across Pangaea
ARTICLE https://doi.org/10.1038/s41467-018-07623-x OPEN Physical and environmental drivers of Paleozoic tetrapod dispersal across Pangaea Neil Brocklehurst1,2, Emma M. Dunne3, Daniel D. Cashmore3 &Jӧrg Frӧbisch2,4 The Carboniferous and Permian were crucial intervals in the establishment of terrestrial ecosystems, which occurred alongside substantial environmental and climate changes throughout the globe, as well as the final assembly of the supercontinent of Pangaea. The fl 1234567890():,; in uence of these changes on tetrapod biogeography is highly contentious, with some authors suggesting a cosmopolitan fauna resulting from a lack of barriers, and some iden- tifying provincialism. Here we carry out a detailed historical biogeographic analysis of late Paleozoic tetrapods to study the patterns of dispersal and vicariance. A likelihood-based approach to infer ancestral areas is combined with stochastic mapping to assess rates of vicariance and dispersal. Both the late Carboniferous and the end-Guadalupian are char- acterised by a decrease in dispersal and a vicariance peak in amniotes and amphibians. The first of these shifts is attributed to orogenic activity, the second to increasing climate heterogeneity. 1 Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK. 2 Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115 Berlin, Germany. 3 School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK. 4 Institut -
Estimating Diversification Rates from the Fossil Record
bioRxiv preprint doi: https://doi.org/10.1101/027599; this version posted September 25, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Estimating diversification rates from the fossil record Gilles Didier1, Marine Fau2 and Michel Laurin2 [email protected], Aix-Marseille Universit´e,CNRS, Centrale Marseille, I2M, UMR 7373, 13453 Marseille, France [email protected], [email protected], CR2P, Sorbonne Universit´es,CNRS/MNHN/UPMC, Mus´eumNational d'Histoire Naturelle, 75005 Paris, France Abstract Diversification rates are estimated from phylogenies, typically without fossils, except in paleonto- logical studies. By nature, rate estimations depend heavily on the time data provided in phylogenies, which are divergence times and (when used) fossil ages. Among these temporal data, fossil ages are by far the most precisely known (divergence times are inferences calibrated with fossils). We propose a method to compute the likelihood of a phylogenetic tree with fossils in which the only known time information is the fossil ages. Testing our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree shape and the fossil dates are almost as accurate as the ones obtained by taking into account all the data, including the divergence times. Moreover they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record). Keywords: speciation rate, extinction rate, fossil ages, maximum likelihood estimation 1 Introduction The history of biodiversity, including evolutionary radiations and mass extinction events, is a central topic of macroevolutionary studies (see for instance Santini et al., 2013; Sidor et al., 2013; Benton et al., 2014, and other works from these authors). -
Heptasuchus Clarki, from the ?Mid-Upper Triassic, Southeastern Big Horn Mountains, Central Wyoming (USA)
The osteology and phylogenetic position of the loricatan (Archosauria: Pseudosuchia) Heptasuchus clarki, from the ?Mid-Upper Triassic, southeastern Big Horn Mountains, Central Wyoming (USA) † Sterling J. Nesbitt1, John M. Zawiskie2,3, Robert M. Dawley4 1 Department of Geosciences, Virginia Tech, Blacksburg, VA, USA 2 Cranbrook Institute of Science, Bloomfield Hills, MI, USA 3 Department of Geology, Wayne State University, Detroit, MI, USA 4 Department of Biology, Ursinus College, Collegeville, PA, USA † Deceased author. ABSTRACT Loricatan pseudosuchians (known as “rauisuchians”) typically consist of poorly understood fragmentary remains known worldwide from the Middle Triassic to the end of the Triassic Period. Renewed interest and the discovery of more complete specimens recently revolutionized our understanding of the relationships of archosaurs, the origin of Crocodylomorpha, and the paleobiology of these animals. However, there are still few loricatans known from the Middle to early portion of the Late Triassic and the forms that occur during this time are largely known from southern Pangea or Europe. Heptasuchus clarki was the first formally recognized North American “rauisuchian” and was collected from a poorly sampled and disparately fossiliferous sequence of Triassic strata in North America. Exposed along the trend of the Casper Arch flanking the southeastern Big Horn Mountains, the type locality of Heptasuchus clarki occurs within a sequence of red beds above the Alcova Limestone and Crow Mountain formations within the Chugwater Group. The age of the type locality is poorly constrained to the Middle—early Late Triassic and is Submitted 17 June 2020 Accepted 14 September 2020 likely similar to or just older than that of the Popo Agie Formation assemblage from Published 27 October 2020 the western portion of Wyoming. -
Evolutionary History of the Butterflyfishes (F: Chaetodontidae
doi:10.1111/j.1420-9101.2009.01904.x Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes D. R. BELLWOOD* ,S.KLANTEN*à,P.F.COWMAN* ,M.S.PRATCHETT ,N.KONOW*§ &L.VAN HERWERDEN*à *School of Marine and Tropical Biology, James Cook University, Townsville, Qld, Australia Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia àMolecular Evolution and Ecology Laboratory, James Cook University, Townsville, Qld, Australia §Ecology and Evolutionary Biology, Brown University, Providence, RI, USA Keywords: Abstract biogeography; Of the 5000 fish species on coral reefs, corals dominate the diet of just 41 chronogram; species. Most (61%) belong to a single family, the butterflyfishes (Chae- coral reef; todontidae). We examine the evolutionary origins of chaetodontid corallivory innovation; using a new molecular phylogeny incorporating all 11 genera. A 1759-bp molecular phylogeny; sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data trophic novelty. yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast-growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline. butterflyfishes (f. Chaetodontidae); of the remainder Introduction most (eight) are in the Labridae.