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Developments in Aquaculture
and Fisheries Science
Volume 41
Biology of Oysters
DEVELOPMENTS IN AQUACULTURE AND
FISHERIES SCIENCE
Brian Bayne
Academic Press is an imprint of Elsevier
125 London Wall, London EC2Y 5AS, United Kingdom
525 B Street, Suite 1800, San Diego, CA 92101-4495, United States
50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States
The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including
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the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions.
This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted
herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in
research methods, professional practices, or medical treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods,
compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the
safety of others, including parties for whom they have a professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or
damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods,
products, instructions, or ideas contained in the material herein.
ISBN 978-0-12-803472-9
ISSN 0167-9309
v
vi Contents
5.3. Ventilation, Particle Capture, and 7.4.4. Gametogenesis and Spawning 450
Clearance 235 7.4.5. Energy Allocations 451
5.3.1. Particle Filtration and Ambient 7.4.6. The Testing of Bioenergetics
Water Flow 235 Models 454
5.3.2. Measuring Feeding Behavior 7.5. Stoichiometry and Growth 457
in the Field 243 7.6. Dynamic Energy Budget Models 469
5.3.3. Particle Capture and Clearance 250 7.6.1. The Standard DEB Model,
5.4. The Functional Morphology of Digestion With an Emphasis on Bivalves 469
and Absorption 275 7.6.2. Environmental Forcing
5.4.1. The Stomach and Digestive Gland 277 by Temperature and Food 483
5.4.2. Intestinal and Glandular Feces 280 7.6.3. Parameter Estimation and the
5.4.3. Absorption and Absorption General Model for Oyster Growth 483
Efficiency 282 7.6.4. The Validation and Application
5.4.4. Metabolic Fecal Loss 291 of DEB Models of Bivalves 485
5.5. Modeling Feeding Behavior 292 7.7. Comparing DEB and Scope
5.5.1. Optimal Feeding Models 292 for Growth (SFG) Models 491
5.5.2. Guts as Chemical Reactors 295 Bibliography 494
5.5.3. Stoichiometry Models 298
5.5.4. A Mechanistic Model 8. Temperature Effects and Other
of Absorption and Gut Transit Time 305 Manifestations of Stress 505
5.5.5. The Geometric Framework 306
5.5.6. The Inducible Response 8.1. Introduction 505
to Predators as a Cost of Feeding 311 8.2. Temperature Effects 506
Bibliography 314 8.2.1. Oxygen- and Capacity-Limitation
of Thermal Tolerance 509
8.2.2. The Heat-Shock Response 511
6. Metabolic Expenditure 331
8.2.3. Methodology 513
6.1. Introduction 331 8.2.4. Two Examples: An Antarctic
6.2. Respiration and the Regulation of Oxygen Bivalve and the European Flat
Uptake 332 Oyster 514
6.3. Levels of Metabolic Rate 336 8.2.5. Mitochondria and Thermal
6.3.1. Components of Standard Tolerance 520
(and Substandard) Metabolic Rate 338 8.2.6. Temperature and the Transcriptome 525
6.3.2. Maintenance Metabolic Rate 355 8.2.7. Ecological Limits 538
6.3.3. Routine Metabolic Rate: 8.3. The Effects of Multiple Environmental
The Effects of Body Size and Genetic Factors on Growth 541
and Feeding 358 Bibliography 554
6.4. Nitrogen Excretion 395
Bibliography 403 9. Reproduction 565
9.1. Introduction 565
7. Growth 417
9.2. Gamete Production 565
7.1. Introduction 417 9.2.1. Hermaphroditism, Sex-Change,
7.2. Measuring Shell Growth 418 and Sex-Ratios 565
7.2.1. Shell-Marking Techniques 418 9.2.2. The Reproductive Cycle 576
7.3. The Description of Growth 427 9.2.3. Spawning and Fertilization 591
7.3.1. The von Bertalanffy Growth 9.2.4. Nutrition, Storage Cycles, and
Model 427 Gametogenesis 600
7.3.2. Growth Models, Aspects 9.2.5. Fecundity and Reproduction
of Life History, and Some Costs, Effort, and Value 610
Bioenergetics 432 9.3. The Oyster Larva 617
7.4. Bioenergetics Models 436 9.3.1. Larval Development and Nutrition 617
7.4.1. Food Consumption 440 9.3.2. Swimming, Settlement, and
7.4.2. Respiration 447 Metamorphosis 655
7.4.3. Excretion 448 Bibliography 683
Contents vii
10. Oysters and the Ecosystem 703 10.6.2. Biodeposition and Nutrient
Cycles 761
10.1. Introduction 703 10.6.3. Biodiversity 774
10.2. Oysters as Keystone Species 10.6.4. Valuing Ecological Services 792
and Ecological Engineers 704 10.7. Carrying Capacity 793
10.3. The Decline of Oysters 709 10.7.1. Statistical Models 794
10.3.1. Baselines, Shifting 10.7.2. Biomass/Production
and Otherwise 709 Relationships and Self-Thinning 795
10.3.2. Population Changes 711 10.7.3. Biofiltration and the
10.3.3. Global Declines in Oyster Food Supply 797
Numbers 721 10.7.4. Box Models 798
10.3.4. Local Declines 723 10.7.5. Fully Spatial Models 803
10.4. Oysters and Ecosystem Trophic 10.7.6. Other Models 808
Networks 729 Bibliography 818
10.5. The “Structured Habitats”
of Oysters 739
10.6. Ecosystem Functions and Services 745
10.6.1. Biofiltration 747 Index 835
This page intentionally left blank
Preface
The time seems right to try to condense into one place an account of research on oysters, as a contribution to current
advances and new opportunities for understanding how they “make a living.” The advances are in two areas, function
at the molecular level and the part played by bivalves in the ecology of coastal seas. Knowledge at the organismal level
provides the bridge between these two areas of research. However, the information is in danger of being lost to working
scientists because of its shear mass and the variety of outlets in which it is published. Edible oysters (the family Ostreidae)
are my focus of attention because they are significant in aquaculture and in the ecology of the coastal benthos, and because
they serve increasingly as experimental models for functional analysis. In a recent bibliometric survey, Guo, Xu, Feng, and
Zhang (2016) used the Science Citation Index to identify 11,493 publications on these oysters between 1991 and 2014
(9604 research articles, 694 meeting abstracts, and 400 reviews). The articles were in 1463 journals, 1259 of which
had published <10 relevant papers. And 10 countries were noted as publishing more than 250 of these papers, including
3960 in the United States, 1456 in France, 888 in China, 566 in Japan, and 274 in Brazil.
Aquaculture currently contributes approximately half of the fish (finfish þ shellfish) consumed worldwide and has been
described as the most vibrant sector of the global food system (Troell et al., 2014). Reports by the Food and Agriculture
Organisation of the United Nations (FAO) attest to an increasingly important role for oysters in aquaculture. For example,
the Pacific oyster, Crassostrea gigas (Thunberg, 1793), due to its potential for rapid growth and tolerance of a wide range of
environmental conditions, has become the species of choice for cultivation in many regions of the world. From its origins in
Japan and following widespread introductions elsewhere (Guo, 2009) its worldwide aquaculture production continues to
expand, from 156,000 tonnes in 1950 to 437,000 per annum by 1970, 1.2 million tonnes in 1990 and reaching nearly 4.5
million tonnes 13 years later (FAO Fisheries and Aquaculture Department: Cultured Aquatic Species Information Pro-
gramme). A related species, the Eastern oyster Crassostrea virginica (Gmelin, 1791), has been harvested for many years
in the United States but now, following the introduction of C. gigas, accounts for less than 35% of the total oyster landings
in that country. Other species of Crassostrea, such as C. angulata and C. sikamea (successfully cultured in China and
Japan), the mangrove oysters of the tropics (C. gasar, C. rhizophorae), and oysters in the genera Ostrea and Saccostrea,
also contribute to total oyster landings worldwide that are now in excess of 5.5 million tonnes per annum, or 38% of total
molluscan aquaculture.
The importance of oysters to the coastal ecosystems of the world (especially estuaries) is expressed in a variety of ways.
The three genera that are the subject of this book (Crassostrea, Ostrea, and Saccostrea) are, for different reasons, com-
monly described as ecosystem engineers and/or functional dominants. The topic is discussed in Chapter 10, but the general
features are well known: as filter feeders, oysters facilitate benthic/pelagic exchanges that influence the balance between
production cycles in the water column and in the sediments; their propensity for creating reefs and other surficial hard
substrate (oyster shell) contributes significantly to increased habitat diversity and biodiversity in otherwise soft-sediment
habitats. They are therefore key species in the functioning of coastal ecosystems, the net outcome of which is the provision
of various ecological services that have societal value, in addition to their value as a food.
A knowledge of oysters therefore contributes to two of the most pressing problems facing ecology as a predictive
science—how will climate change affect the security of global food provision, and how will the anticipated changes in
environment influence the biodiversity of coastal systems? Environmental change elicits three overlapping categories
of response in organisms: their inherent phenotypic plasticity may be expressed without involving changes in the genotype;
they may alter their distribution in space to escape unfavorable changes in habitat—and even though oysters are attached
and sessile as adults, the existence of a dispersive larval stage allows for population migration; and, if forced beyond the
limits of effective phenotypic response alone, the genetic structure of the population may alter over time (genetic diver-
sification leading to speciation). Oysters have provided a rewarding research focus in all three topics—phenotypic plas-
ticity, the connectivity between populations, and genetic pattern in spatially distinct populations. Although strictly
aquacultural aspects of oyster biology are not discussed in this book, relevant features of their physiology, reproduction,
and ecology are.
ix
x Preface
Researchers considering oysters as subjects for investigation are immediately struck by the immense volume of
available literature. This book has been written by drawing on many of the publications available in the refereed journals,
but only a small fraction of the whole are discussed in detail. In selecting papers for discussion my aim has been to provide a
convincing sample of the scholarship involved, without any pretence of complete coverage. I have benefited from previous
efforts to do the same, including C.M. Yonge’s “Oysters” (1960: The New Naturalist series, Collins, London), Paul
Galtsoff’s peerless “The American Oyster Crassostrea virginica Gmelin” (1964: US Fish and Wildlife Service Fishery
Bulletin 64), and many of the chapters in “The Eastern Oyster Crassostrea virginica” edited by Victor Kennedy, Roger
Newell, and Albert Eble (1996: Maryland Sea Grant).
On reading this literature, one issue cannot be ignored. This is a tendency in many published investigations to miss or to
disregard the wider context provided by both theoretical and empirical studies, the latter including other taxa. These missed
opportunities have compromised the ability of the research to meet two challenges: the gain in insight that is possible when
well-judged hypotheses on the interactions between “whole organism” and “molecular” approaches can be formulated; and
the growing demand for computer models that formalize and can be used to predict these effects. Models are essential in
capturing the complexities of ecological systems as they adapt to, or are degraded by, climate change, and they require that
the physiology and behavior of individual organisms be represented. However, the effective inclusion of data on physio-
logical traits to bridge between organismic and molecular approaches, or in making ecological models, depends on a legit-
imacy that is only afforded by appropriate theory. Without this there is a danger of what Levins (writing in 1968) called “an
indigestion of facts” (the problem works both ways: Levins also observed that theoretical work may diverge too far from life
and “become exercises in mathematics inspired by biology rather than an analysis of living systems”). Various examples
are briefly touched upon in this book. Though often understated (due to limits on space), the potential for expressing
soundly based physiological understanding in concepts such as macrophysiology, for example (Chown, Gaston, &
Robinson, 2004; Osovitz & Hofmann, 2007), or individual-based models (Judson, 1994), will be evident to the reader.
But two examples of the drive for legitimacy are worth discussing here (they are covered more fully in relevant chapters).
They both concern the growth of individuals, the first in terms of computer modeling of growth from a knowledge of phys-
iological rates, and the second in terms of the integration between growth and the molecular biology of these traits.
Identifying growth as the difference between rates of energy gain from the food and of metabolic expenditure to ensure
survival has been researched for many years. In Chapter 6 a starting point for discussion is suggested in the application
of von Bertalanffy’s concept of growth as the difference between mass-dependent rates of anabolism and catabolism. From
this simple insight there has grown a large and effective body of theory applied to predicting growth, including the rates
of energy gain and loss by individual organisms, the increase and decline of populations, and the relationships between
these processes and evolutionary fitness. However, doubts concerning the fundamental nature of energy transfers within
organisms, uncertainties arising from empirical representations of the rates of these processes in different species, and
difficulties in describing the dynamics of growth when simulated in this way stimulated the derivation of a more dynamic
description of energy budgeting (Bas Kooijman, 1993, 2010: “Dynamic Energy Budget Theory for Metabolic Organi-
sation,” Cambridge University Press).1 DEB theory now provides the platform of choice for including maintenance,
growth, and reproduction of organisms in ecological models. The narrative of the development of these ideas over the
last 100 years is an instructive example of scientific method and progress. It hinges on the need for a general theory
that predicts the dynamic behavior of species and in circumstances that extend beyond a limited empirical base. Physio-
logical ecologists now possess the means to set their analyses, with confidence, within an appropriate theoretical construct.
The functional biology of oysters and other bivalves has played a key part in the development of these ideas (Chapter 7)
and continues to do so.
A description of the genome of the oyster Crassostrea gigas was published in 2012 by Guofan Zhang and his many
coauthors, a watershed for research on the biology of oysters. From the outset, an emphasis was placed on what the genome
reveals about this oyster’s capacity to resist the stresses imposed by estuaries and the intertidal (the paper was titled “The
oyster genome reveals stress adaptation and complexity of shell formation”). In a subsequent review, Zhang et al. (2016)
described in more detail the genomic response to environmental factors such as temperature, salinity, hypoxia, air exposure,
and exposure to pathogens, and they “. . .used genome analysis to highlight the strong cellular homeostasis system, a unique
adaptive characteristic of oysters.” The authors of these and related studies have been impressed by the large number of
genes or “gene sets” that contribute to defense against physical stressors and potential pathogens. For example, apoptosis
(the physiological process by which organisms maintain an equilibrium between cell proliferation and cell death) is viewed
1. A generalization of mass- and temperature-dependent metabolic relationships to provide a basis for a unified theory of ecology (“Toward a metabolic
theory of ecology”; Brown, Gillooly, Allen, Savage, & West, 2004) is also pertinent here but a discussion is beyond the reach of this book (see Sibly,
Brown, & Kodric-Brown, 2012; Humphries & McCann, 2014).
Preface xi
as a focal process in the oyster’s cellular stress response. The oyster genome revealed 48 genes coding for apoptosis inhib-
itors (Cg—for C. gigas—IAPs), compared with 7 in sea urchins, 5 in Drosophila, and 8 in humans. This finding implied the
presence of an especially complex system to delay cell death and allow time for the repair of cellular damage (in apoptosis,
unlike cell lysis, cell death is regulated or “programmed”): Importantly, “. . .at the molecular level, the expansion, func-
tional diversity and high expression of key gene families [including heat shock protein 70 and the IAPs] are probably central
to the oyster’s adaptation to sessile life in the intertidal zone” (Zhang et al., 2016).
Zhang and colleagues (2016) then ask the following questions: (a) Why are so many defense-related genes found in
oysters? (b) Are these genes all functional, and if so, are they indicative of plasticity in the cell’s stress responses and
involved in acclimation to stress? (c) What roles do these genes play in adaptive differentiation? These questions cannot
be answered by a description of the genome alone; they demand a collaborative effort between molecular geneticists and
physiologists. The techniques available to the molecular biologist include screening the transcription of the genes, silencing
specific genes, and mapping the proteins that are expressed (the proteome) when the organism is exposed to a change in
environment. In a review of proteomics in the study of adaptations to environmental stress Tomanek (2014) describes the
proteome as “. . .a dynamic and complex network that can respond quickly to environmental change and, in many ways,
does so independent of the genome, eg without requiring transcriptional activation.” Responses that do not require mod-
ification of the genomics include a host of posttranslational processes and protein-protein interactions, and these will not be
predicted simply by mapping the transcriptome. Noble (2006: “The Music of Life: Biology beyond the Genome,” Oxford
University Press) makes the wider point elegantly. To paraphrase using his words: “A gene will do one thing in one set of
circumstances and another if circumstances change. . .they operate under control. Genes are controlled by proteins. Those
proteins are in turn coded for by other genes. The genes cannot do what they do without the proteins. And the proteins are
not free agents either. They respond to influences from across the rest of the organism and ultimately from the environment,
too.” This is “downward causation” (see Fig. 1, which is a modification redrawn from Noble, 2006). “So even if we speak of
gene-protein networks, we must be careful. These are not networks that operate independently of higher-level processes.”
Comparisons of the proteome among populations that are experiencing different levels of environmental stress (and
resulting, for example, in differences in the proportional expressions between functional gene families that signal quali-
tatively different impacts on the organism) help to formulate hypotheses for causal relationships between the gene and the
animal’s response. These hypotheses must then be tested by direct investigation of the functional link between genotypic
and phenotypic variation, including individual genes. Oysters have proved to be an effective model in this endeavor. Not
only is there a considerable knowledge base supporting both genomic and physiological investigations, but the resources
of oyster hatcheries can also be employed to produce genetically defined families. Hedgecock, Manahan, and colleagues
(e.g., Hedgecock, McGoldrick, & Bayne, 1995, Hedgecock et al., 2007; Applebaum, Pan, Hedgecock, & Manahan, 2014;
Frieder, Applebaum, Pan, Hedgecock, & Manahan, 2016) demonstrate the power of linked genetic-genomic-physiological
approaches to understanding growth and adaptations to environmental change, using the Pacific oyster. For example,
they warn that experiments with wild-caught individuals subjected to different environmental conditions cannot adequately
control for genotype (G) and genotype environment (E) interactions: “Experiments that manipulate G and, most impor-
tantly, G E, as well as E, to produce phenotypic contrasts that integrate genomic, transcriptomic, proteomic and
Cells Higher-level
controls of gene
expression
Biochemicals pathways
Protein Proteins
machinary
reads genes
Genes
xii Preface
metabolomic with classical biochemical and physiological approaches are required to understand and to predict the
Darwinian responses of organisms to global change.”
The approach described by Noble to understand the functioning organism is not a retreat from reductionism. Rather, it is
a recommendation to concentrate investigations on the points of contact, the interactions and feedbacks, between precisely
defined entities, such as the cell and the matrix of gene-protein interactions. This provides direction to research, and is the
subject of Richard Lewontin’s influential book (2000: “The Triple Helix: Gene, Organism and Environment,” Harvard
University Press). Lewontin argues that every biologist knows that the information in DNA sequences is insufficient to
specify even a folded protein, never mind an entire organism (“. . .if we want to understand which protein is produced
from a gene, we must investigate the complete chain of production in its spatial and temporal detail”); and that organisms
and their environments are in a constant state of flux in which both act as cause and effect in the evolutionary process. There
are many insights in this short book to guide the physiological ecologist who works in collaboration with molecular genet-
icists. For example, Lewontin argues that, as a result of its structural and functional heterogeneity, an organism may be
thought of as a “nexus of a large number of interacting forces that are individually weak.” Experimental science normally
consists of trying to hold most of these forces constant while strongly perturbing one of them to measure its influence. But
it may be misleading then to extrapolate this effect, given a background of many other causal processes acting contem-
poraneously. “Many of the problems of understanding in biology appear when experimental perturbations, chosen because
they can be studied conveniently, are extrapolated to normal circumstances” (Lewontin). The organism in its natural setting
is the appropriate subject of study.
This problem of extrapolation is a serious constraint when applying the results of laboratory experiments to scale phys-
iological responses in the natural environment, and to incorporate physiological traits into ecological models. The point is
illustrated by Angilletta and Sears (2011) in a discussion of the concept of the niche (Lewontin describes the niche as a
flawed metaphor), and in discriminating between the fundamental and the realized thermal niche when attempting to
predict the effects of climate change. The idea that the environment of an organism is causally independent of the organisms
and that “. . .changes in the environment are autonomous and independent of changes in the species itself, is clearly wrong”
(Lewontin). Two aspects can be highlighted (see the review of The Triple Helix by Lloyd, 2004), and both are important in
the biology of oysters. The first is that organisms change their environments by living in them. The gregarious nature of
oysters ensures significant engineering of both their macro- and microenvironments (Chapters 5 and 10). The second is
related but more nuanced. The organism defines its own environment by its phenotypic poise, determining what features
are important for its own survival and performance. It follows that the concept of the niche as a collection of physical and
biological features that may or may not be inhabitable by the organism is unhelpful. Angilletta and Sears (2011) concluded
that “perhaps the best way to circumvent this problem would be to model the niche as an emergent property of a phenotype
interacting with its environment.” The current generation of “mechanistic niche models” does this by using the empirical
knowledge base, formalized in dynamic (and stoichiometrically balanced) submodels, to suggest hypothetical relationships
between environmental factors and physiological performance (Kearney & Porter, 2009). The testing of these models
requires measurements of performance (growth, reproduction, and survival) and their monitoring in the natural envi-
ronment. This is familiar territory for the physiological ecologist whose research can now be enriched by matching the
results to changes in the expression of specific genes.
This book is intended as an account of some of what we know (and some of what we do not know but may infer from
studies of other species) of the biology of oysters, including their phylogeny, evolution, ecology, and physiology, and of the
mechanistic models that are proposed for encapsulating this knowledge in a format useful for prediction. There are gaps in
the coverage, four in particular. The book offers no advice on how to prepare oysters for the table (of the many texts
available, try “Consider the Oyster” by MFK Fisher, 1988: North Point Press, New York; and for a wider historical
treatment see “Oyster: A World History” by Drew Smith, 2010: The History Press, Stroud). The aquaculture of oysters
is not considered because this is covered in detail elsewhere (e.g., “Bivalve Molluscs: Biology, Ecology and Culture”
by Elizabeth Gosling, 2003: Fishing News Books, Oxford). However, this gap extends to research on the restoration of
degraded or lost oyster habitat, which is a timely and popular topic and a test bed of ideas on how oysters affect and
are affected by their environment and the ecosystem (e.g., “Shellfish Aquaculture and the Environment,” edited by Sandra
Shumway, 2011: Wiley and Sons, Chichester). Regretfully, neither space nor time allowed me to include a discussion
of this important subject (but see the journal “Restoration Ecology,” published for The Society for Ecological Restoration).
I also regret not being able to include disease, for the same reasons (“Infectious Disease in Aquaculture: Prevention and
Control,” edited by Brian Austin, 2012: Woodhead Publishing, Oxford). I am aware that an account of the ecology of
oysters that does not include disease does not do full justice to the subject, since disease-mediated mortality has been
(and still is) a significant cause in the decline of oyster stocks worldwide, and a constraint on efforts to cultivate oysters
given the ubiquitous existence of pathogens.
Preface xiii
The fourth area that I do not include is the genomics and molecular biology of oysters. The book was specifically
planned as an account of the biology of oysters, primarily at the organismal level, in the hope that this would contribute
to future developments by providing some context, along the lines discussed above, for the very rapid growth in molecular
research. I know of other researchers who will in time extend the present narrative into these new and exciting areas.
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Acknowledgments
My first and most sincere appreciation is to my family, especially my wife Marianne, who have tolerated my seclusions
with patience and grace. Many friends read various sections, not to correct my mistakes but to advise me on the form the
book was taking and the direction of travel. I acknowledge Dennis Hedgecock, Jerry Hilbish, Richard Koehn, Donal
Manahan, Enrique Navarro, and Tony Underwood. Sandy Shumway helped in the interface with the publishers, and Ellie
Kramer-Taylor helped with getting permissions to reproduce illustrations, and Eric Heuple for the cover design. My thanks
to all the Journals and the Publishers that gave their permission to use their illustrations in the Figures for this book. Tony
Underwood and Gee Chapman provided encouragement from the start. I could not have progressed beyond the first page
without access to the amazing resources of the Library of the University of Sydney and the National Library of Scotland in
Edinburgh. Finally, I dedicate the book to my grandchildren Eren and Ula, as evidence that I did at last complete Chapter 9.
xv
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Chapter 1
Phylogeny
Within certain limits, defined by the fact that the shell consists of two hinged valves, oysters are among the most plastic
organisms known
Gunter (1954)
The oysters are probably the most difficult single group of macrofossils to classify
Cleevely and Morris (1987)
1.1 INTRODUCTION
The view expressed by Cleevely and Morris (1987) and quoted above is widely shared by others who would welcome a
coherent and enduring system of classification that includes both fossil and living oysters. Stenzel (1971) wrote of a
“. . .protean diversity of form in the family Ostreidae, displayed even within well-defined, geographically and genetically
isolated, living oyster species [and which] is not amenable to easy classification.” It is now commonplace for research
papers to start with a similar remark. For example, the taxonomy of oysters “. . . is difficult and often inaccurately deter-
mined because of the high level of phenotypic plasticity of the shell morphology” (Xia, Wu, Xiao, & Yu, 2014); this is often
followed by a proposal for a new or modified phylogeny based on molecular characters. The use of molecular sequences
has expanded rapidly as more potential markers of genealogical relationships have been identified, and the technology that
can recognize and analyse their distribution amongst taxa has developed in parallel. Attempts to discern the phylogeny of
groups of organisms can be traced from the use of allozymes (enzymes encoded by different alleles of the same locus),
thence of targeted genes in the mitochondrial and nuclear genomes, and the current phase of phylogenomics in which mul-
tiple gene loci and even entire genomes can be searched for their application in phylogenetic reconstruction (Dunn et al.,
2008; Boore & Fuerstenberg, 2008). At each step in this progress there has been the challenge of incongruence between
different markers in the phylogenetic patterns that are resolved statistically, between morphological and molecular char-
acters, and between genetic loci.
In this chapter I discuss aspects of the search for clarity in the phylogeny of oysters, in which morphological and
molecular characters have been employed both separately and together. The heuristic power of molecular phylogenetics
is impressive; the morphological and ecological contexts in which phylogenetic resolution is set are rich and complex; and
the search for the relevant evolutionary processes involves knowledge across a wide range of research endeavor—the fossil
record, speciation, life history, larval dispersal, population structure, and the geography of oyster distributions. Multilocus
genomic analysis is bringing new clarity to phylogenetic relationships within the Mollusca in general (Smith et al., 2011)
and the Bivalvia in particular (Bieler et al., 2014; Plazzi, Ceregato, Taviani, & Passamonti, 2011; González et al., 2015) and
with the promise of doing so for families of oysters. Phylogenetic analysis at any taxonomic level (among populations,
species and/or higher taxa) is an exercise in hypothesis setting. Testing predictions for genealogical relations inevitably
involves the underlying ecological and evolutionary processes that determine the proposed phylogenetic pattern. And
resolving these relationships will continue to challenge an understanding of the biology of oysters, in all its aspects.
The likely benefits include the conservation of stocks and maintenance of biodiversity, and in understanding the evolu-
tionary trends in this important group of animals.
1. The change from an aragonitic to a predominantly calcitic shell coincident with a change in water chemistry may have been linked to adaptive changes
in life habit or due to the increased metabolic costs of secreting a calcite shell when the medium was aragonitic, and vice versa (Hautmann, 2006). In
comparative experiments the mineralogical composition of the shell had consequences for the shells’ mechanical properties (fracture strength); the calcitic
shells of oysters were considerably weaker than those of species with aragonitic shells. However, Hautmann (2006) found no association between shell
mineralogy and either a change in morphology or in the mode of life.
Phylogeny Chapter 1 3
PANEL 1.1 A Diagnosis and Classification of Oysters (Based on Hautmann, 2001; Littlewood, 1994)
Term Description
Monomyarian Having one adductor muscle, the ancestral anterior adductor having been lost
Bourrelets The attachment surface for the lateral ligament on the valves at the apex (hinge) of the shell, raised on the
left valve, recessed on the right valve
Byssus Threads attaching the larva to the substrate at metamorphosis; retained in some bivalves (e.g., mussels)
into the adult stage, but lost in oysters and functionally replaced by an adhesive produced by the mantle
lobes
Chomata Ridges on the right valve with corresponding pits on the left valve
Gill: Ascending and descending folds (lamellae) of the gills are linked by tissue connections between gill fil-
Pseudolamellibranch aments (Chapter 5). Oysters are pseudo-lamellibranch because these tissue connections are not as
extensive as in other eulamellibranch species. In filibranch bivalves (e.g., mussels, scallops) gill lamellae
are linked by interlocking cilia, not by tissue connections
Hinge teeth Projections of the shell at the hinge; present in the larva but lost in the adult and functionally replaced by
the folded (tongue-and-groove) nature of the ligament
Continued
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It must be noted that Salamanca’s name was not in the list of
Ministers suggested by Narvaez. The Queen wished it to be added,
but Narvaez declined to follow suit, as he knew that this statesman
was supported by Bulwer, whose dislike of the King was well known;
and the way he had spoken of Francisco before his wedding
naturally made the King averse to seeing him.
Bulwer worked with Bermejo against Isabella during the
premiership of Salamanca, and the publication in The Times of a
demand for the royal divorce was due to him.
At last Francisco and Isabella were reconciled. It was on October
13 that the King returned to the capital. He entered the gate of the
palace in a carriage drawn by six horses, with a mounted escort of
the Guardia Civil. He was dressed quietly in black, and Brunelli, the
Pope’s Legate, was seated on his left. Narvaez, Count Alcoy, Count
Vistahermosa, rode by the coach, and two carriages followed with
the high dignitaries of the palace.
The King looked pleased. General Serrano, whom he hated so
cordially, had left Madrid, and the Queen was waiting for him at the
window. Brunelli was about to follow the royal couple as they walked
away after their first meeting, but Narvaez said: “Whither away, Your
Eminence? Let them be alone with their tears and kisses. These
things are done better without witnesses.”
The Queen arrived that day at her dwelling in the Calle de las
Rejas. There was a family dinner-party in the evening at the palace,
and, in a private interview with her daughter, Maria Cristina begged
her to be more discreet in future; and she reminded her that although
she had, as a widow, allowed herself to be captivated by a
commoner, whilst she was the wife of the King she had never
allowed her thoughts to wander beyond the circle of her rank and her
duty.
The reckless extravagance of the Queen excited much remark.
Courtiers are still living who recollect seeing Isabella give her
bracelets to the beggars who sometimes infest the courtyard of the
palace.
When Miraflores, who was considered the soul of truth, received
a reckless order from the Queen to dispense a certain amount of
money on some petitioner, he had the sum put in pieces on a table,
and it was only the sight of the large sum which was thus laid before
the Queen which showed her the extravagance of her command.
A great influence was soon found to be at work in the palace in
the person of Sister Patrocinio, whose brother, Quiroga, was one of
the gentlemen-in-waiting.
CHAPTER XI
ATTEMPT ON THE LIFE OF QUEEN ISABELLA—THE OVERTHROW OF THE
QUEEN-MOTHER, MARIA CRISTINA
1850–1854
There was much variety of feeling when it was known that an heir to
the throne was expected. On the day of the birth, July 12, 1850, the
clerics, Ministers, diplomats, officers, and other important
personages of the realm, assembled at the palace to pay their
respects to the expected infant. But the bells and cannon had hardly
announced to the nation the birth of the girl-child when it expired. So
the dead form of the infant, which had only drawn breath in this world
for five minutes, was brought into the assembly of dignitaries, and
after this sad display the gathering dispersed in silence. The kind-
heartedness of the Queen was shown in her thoughtful generosity to
the nurses who were disappointed of their charge.
“Poor nurses, they must have felt it very much!” she exclaimed.
“But tell them not to mind, for they shall be paid the same as if they
had had my child.”
In February, 1852, an heir to the throne was once more expected,
and the birth of the Infanta Isabella was celebrated by the usual
solemn presentation. When the King showed the infant to his
Ministers, he said to the Generals Castaños and Castroterreño:
“You have served four Kings, and now you have a Princess who
may one day be your Sovereign.”
It was on February 2, 1852, that the dastardly attempt was made
on the life of the Queen, just before leaving the palace for the
Church of Atocha, where the royal infant was to be baptized. The
Court procession was passing along the quadrangular gallery, hung
with the priceless tapestries only displayed on important occasions,
when Manuel Martin Merino, a priest of a parish of Madrid, suddenly
darted forward from the spectators lining the way, with the halberdier
guard. The petition in the cleric’s hand and his garb of a cleric led to
his step forward being unmolested, and the Queen turned to him,
prepared to take the paper. But the next moment the other hand of
the assassin appeared from under his cloak with a dagger, which he
swiftly aimed at the royal mother. Fortunately, the Queen’s corset
turned aside the murderous weapon, and, although blood spurted
from her bodice, the wound was not very deep; but she was at once
put to bed and placed under the care of the royal physicians.
The royal infant was promptly seized from the arms of its mother
at the moment of the attack, by an officer of the Royal Guard, and for
this presence of mind the soldier was afterwards given the title of the
Marquis of Amparo.
With regard to the assailant, the Queen said to her Ministers:
“You have often vexed me by turning a deaf ear to my pleas of mercy
for criminals, but I wish this man to be punished immediately.” And,
with the outraged feeling of the object of such a dastardly deed,
Isabella turned to the would-be murderer, and said: “What have I
ever done to offend you, that you should have attacked me thus?”
During the trial in the succeeding days the Queen softened to the
criminal, and said to her advisers: “No, no! don’t kill him for what he
did to me!”
However, justice delivered the man to the hangman five days
after his deed.
The efforts to discover Merino’s accomplices were fruitless, and it
was thought that the deed had been prompted more by the
demagogue party than by the Carlists.
The cool, cynical manner of the cleric never left him even at the
moment of his execution.
When the priest’s hair was cut for the last time, he said to the
barber: “Don’t cut much, or I shall catch cold.”
The doomed man’s request to say a few words from the scaffold
was refused. When asked what he had wished to say, he replied:
“Nothing much. I pity you all for having to stay in this world of
corruption and misery.”
The ovation which the Queen had when she finally went to the
Church of Atocha to present the infant surpasses description.
Flowers strewed the way, and tears of joy showed the sympathy of
the people with the Queen in her capacity as mother, and at her
escape from the attempt on her life.
From 1852 to 1854 Isabella failed to please her subjects, and the
outburst of loyalty which had followed the attempt on her life
gradually waned. Curiously indifferent to what was for her personal
interest, as well as for the welfare of the country, Isabella turned a
deaf ear to the advice of her Ministers to dissolve a Cabinet which
was under the leadership of the Count of San Luis, who was known
to be the tool of Queen Maria Cristina, now so much hated by the
Spaniards. Miraflores wrote a letter to Isabella, advising the return of
Espartero, the Count of Valencia, but the letter never reached its
destination.
Remonstrances which had been made upon the Government
were now directed straight to the Throne.
“You see,” said her advisers, “how the persons whom you have
overwhelmed with honours and favours speak against you!”
The Generals O’Donnell and Dulce finally took an active part
against the Ministry, supported by the Queen-mother and Rianzares.
The Count of San Luis was a man of fine bearing and charming
manners. He had been conspicuous in his early days for his
banquets and gallantries, but he had also been known for many a
generous deed to his friends; and it was noticeable that when the
tide of favour left him he was deserted by all those to whom he had
been of service.
The birth of another royal infant in 1854 excited little or no
interest in the capital, where discontent with the reigning powers was
so evident. General Dulce was accused in the presence of the
Queen and San Luis of having conspired against the Throne. This
the officer indignantly denied on the spot, declaring that never could
he have believed in the perfidy which had prompted the report.
At last the storm of revolution broke over Madrid, and the parties
of the Generals O’Donnell and Dulce came into collision with those
of the Government. Insulting cries against the Queen-mother filled
the streets, and during the three days’ uproar the house of Maria
Cristina, in the Calle de las Rejas, was sacked, as well as those of
her partisans. The furniture was burned in the street, and Maria
Cristina took refuge in the royal palace.
After the Pronunciamento of Vicalvaro and O’Donnell to the
troops, it was evident that the soldiers of the Escorial would also
revolt against the Government.
It was then that Isabella was filled with the noble impulse to go
alone to the barracks of the mutinous regiments and reason
personally with them. With her face aglow with confidence in her
soldiers and in herself, she said: “I am sure that the generals will
come back with me then to Madrid, and the soldiers will return to
their barracks shouting ‘Vivas’ for their Queen.”
But this step, which would have appealed with irresistible force to
the subjects, was opposed by the Ministers, who objected to a
course which would have robbed them of their portfolios by the
Sovereign coming to an understanding with those who were
opposed to their opinions.
T H E C O U N C I L O F M I N I S T E R S O F I S A B E L L A I I . D E C L A R E S WA R
AGAINST MOROCCO
1864–1868