Mathematical Macroevolution in Diatom Research E-Book

Janice L. Pappas

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Diatoms: Biology and Applications
• Sprache: Englisch

Seitenzahl: 908

Veröffentlichungsjahr: 2023

Beschreibung

MATHEMATICAL MACROEVOLUTION IN DIATOM RESEARCH Buy this book to learn how to use mathematics in macroevolution research and apply mathematics to study complex biological problems. This book contains recent research in mathematical and analytical studies on diatoms. These studies reflect the complex and intricate nature of the problems being analyzed and the need to use mathematics as an aid in finding solutions. Diatoms are important components of marine food webs, the silica and carbon cycles, primary productivity, and carbon sequestration. Their uniqueness as glass-encased unicells and their presence throughout geologic history exemplifies the need to better understand such organisms. Explicating the role of diatoms in the biological world is no more urgent than their role as environmental and climate indicators, and as such, is aided by the mathematical studies in this book. The volume contains twelve original research papers as chapters. Macroevolutionary science topics covered are morphological analysis, morphospace analysis, adaptation, food web dynamics, origination-extinction and diversity, biogeography, life cycle dynamics, complexity, symmetry, and evolvability. Mathematics used in the chapters include stochastic and delay differential and partial differential equations, differential geometry, probability theory, ergodic theory, group theory, knot theory, statistical distributions, chaos theory, and combinatorics. Applied sciences used in the chapters include networks, machine learning, robotics, computer vision, image processing, pattern recognition, and dynamical systems. The volume covers a diverse range of mathematical treatments of topics in diatom research. Audience Diatom researchers, mathematical biologists, evolutionary and macroevolutionary biologists, paleontologists, paleobiologists, theoretical biologists, as well as researchers in applied mathematics, algorithm sciences, complex systems science, computational sciences, informatics, computer vision and image processing sciences, nanoscience, the biofuels industry, and applied engineering.

Leseprobe

Contents

Cover

Table of Contents

Series Page

Title Page

Copyright Page

Dedication Page

List of Figures

List of Tables

Preface

Acknowledgments

Prologue – Introductory Remarks

Part I: MORPHOLOGICAL MEASUREMENT IN MACROEVOLUTIONARY DISTRIBUTION ANALYSIS

1 Diatom Bauplan, As Modified 2D Valve Face Shapes of a 3D Capped Cylinder and Valve Shape Distribution

1.1 Introduction

1.2 Methods: A Test of Recurrent Diatom Valve Shapes

1.3 Results

1.4 Discussion

1.5 Summary and Future Research

1.6 Appendix

1.7 References

2 Comparative Surface Analysis and Tracking Changes in Diatom Valve Face Morphology

2.1 Introduction

2.2 Purpose of this Study

2.3 Background on Image and Surface Geometry

2.4 Image Matching Kinematics via the Jacobian

2.5 Methods

2.6 Results

2.7 Discussion

2.8 Summary and Future Research

2.9 References

3 Diatom Valve Morphology, Surface Gradients and Natural Classification

3.1 Introduction

3.2 Purposes of this Study

3.3 Methods

3.4 Diatom Valve Surface Morphological Analysis

3.5 Results

3.6 Discussion

3.7 Summary and Future Research

3.8 References

Part II: MACROEVOLUTIONARY SYSTEMS ANALYSIS OF DIATOMS

4 Probabilistic Diatom Adaptive Radiation in the Southern Ocean

4.1 Introduction

4.2 Purposes of this Study

4.3 Mathematical Modeling of Adaptive Radiation

4.4 Methods

4.5 Results

4.6 Discussion

4.7 Summary and Future Directions

4.8 References

5 Cenozoic Diatom Origination and Extinction and Influences on Diversity

5.1 Introduction

5.2 Purposes of this Study

5.3 Methods and Background

5.4 Results

5.5 Discussion

5.6 Summary and Future Research

5.7 References

6 Diatom Food Web Dynamics and Hydrodynamics Influences in the Arctic Ocean

6.1 Introduction

6.2 Purposes of this Study

6.3 Background on Arctic Ocean Diatoms

6.4 Lattice Boltzmann Model

6.5 Lattice Boltzmann Model and Hydrodynamics

6.6 Lattice Boltzmann Model: Diatom Bloom Density, Sea Ice and Upwelling

6.7 Lattice Boltzmann Model: Specifications for Simulation

6.8 Methods

6.9 Results

6.10 Discussion

6.11 Summary and Future Research

6.12 References

Part III: GENERAL AND SPECIAL FUNCTIONS IN DIATOM MACROEVOLUTIONARY SPACES

7 Diatom Clade Biogeography: Climate Influences, Phenotypic Integration and Endemism

7.1 Introduction

7.2 Purposes of this Study

7.3 Methods

7.4 Results

7.5 Discussion

7.6 Summary and Future Research

7.7 References

8 Cell Division Timing and Mode of the Diatom Life Cycle

8.1 Introduction

8.2 Purposes of this Study

8.3 Background on the Diatom Cell Cycle

8.4 Modeling the Diatom Life Cycle: Timing of Stages and Switches

8.5 Methods

8.6 Results

8.7 Discussion

8.8 Summary and Future Research

8.9 References

9 Diatom Morphospaces, Tree Spaces and Lineage Crown Groups

9.1 Introduction

9.2 Occupied and Unoccupied Morphospace

9.3 Purposes of this Study

9.4 Morphospace Structure and Dynamics

9.5 Phylogeny Structure and Phylogenetic Dynamics

9.6 Measuring Occupied Morphospace: Clustering Coefficients

9.7 A Brief Background on Diatom Morphospaces

9.8 Mathematical Morphospaces in the Context of a Diatom Phylogeny

9.9 Methods

9.10 Results

9.11 Discussion

9.12 Summary and Future Research

9.13 References

Part IV: MACROEVOLUTIONARY CHARACTERISTICS OF DIATOMS

10 Diatom Morphological Complexity Over Time as a Measurable Dynamical System

10.1 Introduction

10.2 Diatom Morphological Complexity

10.3 Purposes of this Study

10.4 Characterizing Morphological Complexity

10.5 Information and Morphology

10.6 Information and Complexity

10.7 Markov Chains and their Properties

10.8 Ergodicity and Chaoticity

10.9 Kolmogorov Complexity and Entropy

10.10 Methods

10.11 Results

10.12 Discussion

10.13 Summary and Future Research

10.14 References

11 Diatom Surface Symmetry, Symmetry Groups and Symmetry Breaking

11.1 Introduction

11.2 Symmetry of 3D Organismal Surfaces

11.3 Symmetry Groups

11.4 Purposes of this Study

11.5 Methods

11.6 Results

11.7 Discussion

11.8 Summary and Future Research

11.9 References

12 Evolvability of Diatoms as a Function of 3D Surface Phenotype

12.1 Introduction

12.2 Purposes of this Study

12.3 Methods

12.4 Results

12.5 Discussion

12.6 Summary and Future Research

12.7 References

Epilogue – Findings and the Future

Index

Also of Interest

Wiley End User License Agreement

List of Tables

Chapter 1

Table 1.1 Basic geometries and diatom examples given for each geometric valve ...

Table 1.2 A diagrammatic and descriptive representation of the width function,...

Table 1.3 Partial valve reconstructions for

Cymbella cistula

in terms of numbe...

Table 1.4 List of 41 diatom taxa used in Legendre shape analysis and source of...

Table 1.5 Valve shapes matched with minimum number of Legendre coefficient use...

Table 1.6 Legendre coefficient number representing valve shape bins, tabulated...

Chapter 2

Table 2.1

Arachnoidiscus

image matching of double ribs. Jacobians, Jacobian de...

Table 2.2

Arachnoidiscus

image matching of

A

.

ehrenbergii

SEM to 3D surface mo...

Table 2.3

Arachnoidiscus

image matching of whole valves. Jacobians, Jacobian d...

Chapter 3

Table 3.1 Sixty-seven naviculoid taxa used in HOG and SVR analyses. Authority ...

Table 3.2 Image gradient components for each pixel intensity in a digital imag...

Chapter 4

Table 4.1 Southern Ocean diatom lineages represented by

Chaetoceros

,

Fragilari

...

Table 4.2 Mean values for

x

and

V

, OU and Lyapunov modified OU, and slice samp...

Table 4.3 Adaptive radiation as niche filling in terms of ecological niche pre...

Table 4.4 Adaptive radiation as niche filling in terms of ecological niche pre...

Table 4.5 Niche filling probability matrix of ecological niche preference and ...

Chapter 5

Table 5.1 Piecewise values and conditions obtained from expansion of the survi...

Table 5.2 Piecewise values and conditions obtained from expansion of the cumul...

Table 5.3 Cumulative functions as least-squares fitted

n

th

-order polynomials f...

Table 5.4 Piecewise values and conditions obtained from expansion of the survi...

Table 5.5 Relative maxima ages for Cenozoic diatom origination and extinction ...

Table 5.6 Interarrival (origination) and arrival (extinction) values for Poiss...

Table 5.7 Non-reversal ages for origination and extinction and the Lyapunov ra...

Table 5.8 Piecewise values and conditions obtained from expansion of the survi...

Table 5.9 Diversity interarrival (relative minima ages) and arrival (relative ...

Table 5.10 Non-reversal ages for diversity relative maxima or relative minima ...

Table 5.11 Poisson process and Lyapunov process results for combination origin...

Chapter 6

Table 6.1 Percent lipid biomass for nine dominant Arctic diatom genera.

Table 6.2 Characteristics of Arctic diatom genera for LBM simulations.

Table 6.3 Arctic Ocean summary characteristics used in LBM simulation.

Chapter 7

Table 7.1 Köppen climate classification category (with additions from the Hold...

Table 7.2 Shortest tour lengths of clades over all continents.

Table 7.3 Abbreviated temperature, humidity, precipitation, and vegetation con...

Chapter 9

Table 9.1 Basic valve shapes, descriptions and Legendre coefficient bins.*

Table 9.2 Taxonomic, crown group and Legendre coefficients assigned to 128 gen...

Table 9.3 NMDS ordination results of STRESS and coefficients of determination.

Table 9.4 Table of rescaled NMDS equations for each submorphospace bounded by ...

Table 9.5 Clustering coefficients as occupied submorphospace for each crown gr...

Chapter 10

Table 10.1 Characteristics of structural and algorithmic information theories.

Table 10.2 Diatom taxa with respect to the fossil record* and entropy values.

Table 10.3 Lyapunov exponents, sum and determinant.

Table 10.4 For Cretaceous taxa, Kolmogorov complexity relative taxon order fro...

Table 10.5 For Cenozoic taxa, Kolmogorov complexity relative taxon order from ...

Table 10.6 For all taxa, Kolmogorov complexity relative taxon order from most ...

Chapter 11

Table 11.1 Composite compilation of knot symmetry classification by [11.9.21.]...

Table 11.2 Surface models constructed via systems of parametric 3D equations f...

Table 11.3

Actinoptychus

values for

u

and

v

and Eigenvalues of the inverse Jac...

Table 11.4

Arachnoidiscus

values for

u

and

v

and Eigenvalues of the inverse Ja...

Table 11.5

Campylodiscus

values for

u

and

v

and Eigenvalues of the inverse Jac...

Table 11.6

Cocconeis

values for

u

and

v

and Eigenvalues of the inverse Jacobia...

Table 11.7

Cyclotella

values for

u

and

v

and Eigenvalues of the inverse Jacobi...

Table 11.8

Cylindrotheca

values for

u

and

v

and Eigenvalues of the inverse Jac...

Table 11.9

Entomoneis

values for

u

and

v

and Eigenvalues of the inverse Jacobi...

Table 11.10

Surirella

values for

u

and

v

and Eigenvalues of the inverse Jacobi...

Table 11.11

Tabularia

values for

u

and

v

and Eigenvalues of the inverse Jacobi...

Table 11.12 Best-fit equations for genera of symmetry breaking (

Br

) with respe...

Table 11.13 Symmetry group and breaking rates obtained from 6

th

-order polynomi...

Table 11.14 Best-fit equations for size reduction curve fits of apical length ...

Table 11.15 Size reduction rates from curves plotted of apical length (

l

) vers...

Chapter 12

Table 12.1 The

z

-equations for

Actinoptychus

,

Arachnoidiscus

and

Cyclotella

. F...

Table 12.2 Phenotypic surface features, mathematical operator and numerical re...

Table 12.3 Results from calculation of Christoffel symbols for

Actinoptychus

,

Table 12.4 Results from calculation of the Hessian and the Laplacian for

Actin

...

Table 12.5 Hessian and Laplacian

x

,

y

,

z

eigenvalues for

Actinoptychus

,

Arachn

...

Table 12.6 Sum of the Christoffel symbols that are different among genera at

u

Table 12.7 Values of the phenotype gradient in the

z

-value from the Hessian at...

Table 12.8 Phenotypic robustness as the dot product of the phenotype gradient ...

Table 12.9 Hessian and Laplacian

z

eigenvalues for

Actinoptychus

,

Arachnoidisc

...

Table 12.10 The Hessian determinants from the

z

-values.

Table 12.11 Values from additive fitness functions for all genera and contribu...

Table 12.12 Values for comparative evolvability based on fitness decrease and ...

Guide

Cover Page

Frontmatter

Frontmatter

Title Page

Copyright

Dedication

Epilogue

List of Figures

List of Tables

Preface

Acknowledgments

Prologue – Introductory Remarks

Table of Contents

Begin Reading

Index

Also of Interest

Wiley End User License Agreement

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Scrivener Publishing100 Cummings Center, Suite 541JBeverly, MA 01915-6106

Diatoms: Biology and Applications

Series Editors: Richard Gordon ([email protected]) and Joseph Seckbach ([email protected])

Scope: The diatoms are a single-cell algal group, with each cell surrounded by a silica shell. The shells have beautiful attractive shapes with multiscalar structure at 8 orders of magnitude, and have several uses. 20% of the oxygen we breathe is produced by diatom photosynthesis, and they feed most of the aquatic food chain in freshwaters and the oceans. Diatoms serve as sources of biofuel and electrical solar energy production and are impacting on nanotechnology and photonics. They are important ecological and paleoclimate indicators. Some of them are extremophiles, living at high temperatures or in ice, at extremes of pH, at high or low light levels, and surviving desiccation. There are about 100,000 species and as many papers written about them since their discovery over three hundred years ago. The literature on diatoms is currently doubling every ten years, with 50,000 papers during the last decade (2006-2016). In this context, it is timely to review the progress to date, highlight cutting-edge discoveries, and discuss exciting future perspectives. To fulfill this objective, this new Diatom Series is being launched under the leadership of two experts in diatoms and related disciplines. The aim is to provide a comprehensive and reliable source of information on diatom biology and applications and enhance interdisciplinary collaborations required to advance knowledge and applications of diatoms.

Publishers at ScrivenerMartin Scrivener ([email protected])Phillip Carmical ([email protected])

Mathematical Macroevolution in Diatom Research

Janice L. Pappas

Department of Mathematics, University of Michigan, Ann Arbor, MI, USA

This edition first published 2023 by John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA and Scrivener Publishing LLC, 100 Cummings Center, Suite 541J, Beverly, MA 01915, USA© 2023 Scrivener Publishing LLCFor more information about Scrivener publications please visit www.scrivenerpublishing.com.

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Library of Congress Cataloging-in-Publication Data

ISBN 978-1-119-74985-1

Cover images: Tiling of 3D diatom surface models and partial diatom arrangement from the frontispiece by Janice L. Pappas Frontispiece: An artful arrangement of 3D diatom surface models by Janice L. Pappas in the spirit of the art form of diatom arranging from the Victorian era, Klaus Kemp and Dr. Stephen S. NagyCover design by Russell Richardson

To Emmy, Jamie, Olaf, and a host of flying miracles, at once, lively and peaceful.