Abstract
The fossil record is the only source of information on the long-term
dynamics of species assemblages. Here we assess the degree of
ecological stability of the epifaunal pterioid bivalve assemblage
(EPBA), which is part of the Middle Devonian Hamilton fauna of New York
�the type example of the pattern of coordinated stasis, in which long
intervals of faunal persistence are terminated by turnover events
induced by environmental change. Previous studies have used changes in
abundance structure within specific biofacies as evidence for a lack
of ecological stability of the Hamilton fauna. By comparing data on
relative abundance, body size, and predation, indexed as the frequency
of unsuccessful shell-crushing attacks, of the EPBA, we show that
abundance structure varied through time, but body-size structure and
predation pressure remained relatively stable. We suggest that the
energetic set-up of the Hamilton fauna's food web was able to
accommodate changes in species attributes, such as fluctuating prey
abundances. Ecological redundancy in prey resources, adaptive foraging
of shell-crushing predators (arising from predator behavioral or
adaptive switching in prey selection in response to changing prey
abundances), and allometric scaling of predator-prey interactions are
discussed as potential stabilizing factors contributing to the
persistence of the Hamilton fauna's EPBA. Our study underscores the
value and importance of multiple lines of evidence in tests of
ecological stability in the fossil record.
Citation: Nagel-Myers J, Dietl GP, Handley JC, Brett CE (2013)
Abundance Is Not Enough: The Need for Multiple Lines of Evidence in
Testing for Ecological Stability in the Fossil Record. PLoS ONE 8(5):
e63071. doi:10.1371/journal.pone.0063071
Editor: David L. Roberts, University of Kent, United Kingdom
Received: January 2, 2013; Accepted: March 28, 2013; Published: May
15, 2013
Copyright: � 2013 Nagel-Myers et al. This is an open-access article
distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and
reproduction in any medium, provided the original author and source
are credited.
Funding: There are no current external funding sources for this study.
Competing interests: The authors have declared that no competing
interests exist.
Introduction
Understanding how the structure and function of ecological communities
changes or remains the same through time is a topic of considerable
interest [1], [2]. Much of what we know about community stability and
change comes from insights gained from ecological data collected over
short time intervals of up to a few decades [2]�[5]. Increasingly,
however, the fossil record has proven to be a valuable ecological
archive of faunal responses to disturbances over long temporal scales
not available in ecological studies [2], [6], [7]. One of the most
surprising insights gained from paleoecological data is that some
fossil assemblages may remain relatively stable over millions of
years.
The faunas of the Middle Devonian Hamilton Group of New York State
provide an exemplar of this pattern. Brett and Baird [8] recognized
long intervals of faunal persistence terminated by turnover events
induced by environmental change (see also [9]�[11]). Nearly two
decades of additional research has generally supported the original
interpretation of taxonomic stasis in this fauna [10], [12]�in other
words, large numbers of species, or closely related species groups
within lineages, persist in similar facies/environments over long
intervals of time.
A less well-documented pattern in the fossil record is the suggestion
that faunas are also relatively stable in terms of ecology (ecologic
stasis; sensu [12]). This claim has been subject to considerable
discussion [13]�[17]. For instance, although guild structure appears
to persist in the Hamilton fauna [10], [12], [18], several studies
have challenged ecological stability expressed in terms of relative
abundance data (e.g., [19]�[21]).
The unresolved issue in these cases is sample comparability. Valid
comparisons of faunas of differing age, required to test for
properties of ecological stability, have to be based upon the most
similar biofacies; lithology alone is not sufficient. Incomplete
sampling and small-scale spatial variation in faunas and environments
can further obscure paleoecological data [11], [12]. Two extensive
studies recently corroborated ecological stability within specific
biofacies of the Hamilton fauna. For instance, Brett et al. [10]
showed that guild proportions remained similar in all samples of five
biofacies, ranging from relatively low diversity, dysoxic assemblages
to highly diverse coral- and brachiopod-rich, shallow shelf biotas,
and Ivany et al. [12] documented the constancy of the relative
abundance of the diverse coral-brachiopod biofacies in 13 horizons
throughout a stratigraphic interval spanning about 5 to 5.5 million
years.
Here we expand upon our current understanding of the pattern of
ecological stability in the fossil record. Our approach compares data
on abundance structure (the standard metric used to test for
ecological stability in the fossil record), body-size structure, and
predation pressure in bivalve-dominated assemblages within the well-
constrained stratigraphic framework of the Hamilton fauna [10], [22].
Study system
To test for the pattern of ecological stability we focused on a
particular biofacies�that of shallow, storm-affected, silty shelf
bivalve-dominated assemblages�of the well-preserved Middle Devonian
Hamilton fauna of New York. The Hamilton fauna comprises over 300
invertebrate species [10], [23]�[27] and occurs throughout four
formations (Fig. 1): Oatka Creek, Skaneateles, Ludlowville, and
Moscow, each of which is approximately a 3rd-order cycle of sea-level
change lasting ~1�2.0 million years [18], [27]. These units represent
shallow subtidal muddy to silty shelf sediments deposited below fair
weather wave base, but above storm wave base in, euphotic to dysphotic
environments, ranging in water depth from about 20 to 80 meters in a
warm temperate to subtropical setting [10], [23], [28]. Each of the
formations is divisible into a series of 10�20 m scale, coarsening
upward mudstone to siltstone members and submembers representing 4th-
order cycles of sea-level change of ~400 ka duration (Fig. 1; [22]).
Average rates of sea-level rise during this time interval have been
estimated to be around 1 to 10 mm/year based on estimates of absolute
depth change of ~40�50 m [22], [26], [28] and durations of decameter
scale submembers [29]. Our study system included seven localities
collected within a 2000 km2 geographic area, examined a duration of
about 800 ka, and sampled three 4th-order depositional cycles�Giv-1A,
Giv-1B, and Giv-1C�from the lower Givetian Skaneateles Formation (Fig.
1).
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Figure 1. Sequence stratigraphy for the Middle Devonian of New York
State.
doi:10.1371/journal.pone.0063071.g001
We targeted a functional group of suspension feeding bivalves within
the bivalve-dominated biofacies of the Hamilton fauna�the epifaunal
pterioid bivalve assemblage (hereafter referred to as EPBA), which is
composed of pterioid species that flourished in the Devonian [30].
Pterioid bivalves lived either byssally attached (Pseudaviculopecten)
or reclining (Ptychopteria, Leptodesma, and Actinopteria) on soft
substrates (Fig. 2). These genera reflect either single species or
morphological groups of closely-related species, which comprised as
much as 75% of the shallow water shelly epibenthos [31], [32]. As in
many modern marine systems, this functional group would have played a
key role in ecosystem function, influencing nutrient dynamics, as well
as serving as food for higher trophic levels [33]. Co-occurring with
this functional group of bivalves was a moderate diversity of sessile,
epifaunal suspension-feeding brachiopods, bryozoans, and crinoids,
endobenthic scavengers, such as trilobites and gastropods, and deposit
feeders, including nuculid bivalves, with moderate bioturbation [34].
The presence of benthic, durophagous (shell-crushing) predators, such
as phyllocarid crustaceans and gnathostome fishes [35], [36] is
preserved in the rich trace fossil record of their attacks on bivalve
prey (Fig. 3; [36]).
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Figure 2. Reconstruction of epifaunal pterioid bivalve assemblage of
the Hamilton fauna.
doi:10.1371/journal.pone.0063071.g002
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Figure 3. Examples of predation-induced shell repair.
Left: Ptychopteria from Cole Hill (PRI 67471); Right:
Pseudaviculopecten from Oran Gulf (PRI 67470); Center: close-up view
of repaired shell portion of each specimen; note off-setting of
ribbing patterns and high relief of repair scars.
doi:10.1371/journal.pone.0063071.g003
This predator-prey interaction forms a simple food-web module (sensu
[37]) in which to test for ecological stability in abundance, body
size, and predation in the Hamilton fauna's EPBA. This �module�
approach is widely used in community ecology to help disentangle the
complexity of a system by focusing on individual building blocks
(e.g., specific species interactions) as a proxy for the dynamics of
the whole system [38], [39].
Results
Abundance
The most abundant species in the EPBA was Actinopteria (55.6%; n =
299), followed by Ptychopteria (34.4%; n = 184), Leptodesma (5%; n =
28), and Pseudaviculopecten (5%; n = 27). Relative abundances of EPBA
species varied from 15.3�63.8% for Actinopteria, 25.6�71.2% for
Ptychopteria, 2.6�8.5% for Leptodesma, and 2.6�5.5% for
Pseudaviculopecten, throughout the stratigraphic section (Table S1).
Model ranking results using Akaike's Information Criterion (AIC)
indicate 99.9% support for a change in relative abundance structure of
the EPBA across all stratigraphic units; Bayesian Information
Criterion (BIC) scores, which are less sensitive to model complexity,
also indicate�with 96.7% support�that relative abundances of the EPBA
differ across stratigraphic units (Table 1).
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Table 1. Model ranking results for change in relative abundances.
doi:10.1371/journal.pone.0063071.t001
Body size
The average body size of the 538 bivalve specimens we examined was
28.9 mm. Average body size varied between 24.8 to 27.9 mm for
Actinopteria, 32.5 to 35.8 mm for Ptychopteria, 29.4 to 40.0 mm for
Leptodesma, and 29.7 to 34.5 mm for Pseudaviculopecten, throughout the
stratigraphic section (Fig. 4; Table S2). Deviance and residual
degrees of freedom indicate that all proposed regression models have
good fits (Table 2). Model ranking results using AIC and BIC indicate
no support (<0.1%) for a change in body-size structure of the EPBA
across all time units (Table 2). Locality also has no effect on body
size (<0.1% using both AIC and BIC; Table 2). Taxon identity, however,
has a significant effect on body size (91% using AIC and 100% using
BIC; Table 2), with Ptychopteria on average the largest (34 mm)
species in the EPBA and Actinopteria the smallest (25 mm; Table S2).
For the interaction model, there is negligible evidence that average
size for each taxon changes across time units (9% and <0.1% using AIC
and BIC, respectively; Table 2).
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Figure 4. Average body-size structure of the epifaunal pterioid
bivalve assemblage through time.
doi:10.1371/journal.pone.0063071.g004
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Table 2. Model ranking results for body size as a function of
stratigraphic unit, locality, and taxon.
doi:10.1371/journal.pone.0063071.t002
Predation
At least one shell-crushing repair scar was found on 112 of the 538
bivalve specimens examined in our samples (Fig. 5), with an average
repair frequency (RF) of 18.3% for Actinopteria, 19.6% for
Ptychopteria, 32.3% for Pseudaviculopecten, and 9.5% for Leptodesma
(Fig. 5, Table S3). Repair frequency for the EPBA as a whole varied
from 16.9% to 21.8% throughout the stratigraphic section (Fig. 5). All
proposed logistic regression models have good fits based on upon
deviance and residual degrees of freedom (Table 3). Using a threshold
of 10% for significance, neither AIC nor BIC scores show appreciable
support for an influence of time unit on RF (3.3% and 0.2%,
respectively; Table 3). Similarly, an effect of locality and taxon on
RF has little support (0.4% and <0.1% using AIC and BIC, respectively,
for locality; 6.3% and <0.1% using AIC and BIC, respectively, for
taxon; Table 3). There is significant support for an effect of body
size on RF by both ranking methods (76.4% using AIC and 38.8% using
BIC; Table 3), although the biological effect of this influence is
small; the estimated coefficient of size is 0.0279 (std. err. = 0.012;
p = 0.02), which suggests that for every 1 mm increase in size over
the mean size there is an increase in the probability of finding a
repair scar of only 0.005. The interaction model also had no support
(<0.1%) by either AIC or BIC (Table 3) for RF differing across time
units as a function of taxon.
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Figure 5. Average repair frequency of the epifaunal pterioid bivalve
assemblage through time.
doi:10.1371/journal.pone.0063071.g005
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Table 3. Model ranking results for repair frequency as a function of
stratigraphic unit, locality, taxon, and body size.
doi:10.1371/journal.pone.0063071.t003
Discussion
Food-web structure and stability
Our results demonstrate that the body-size structure of, and predation
pressure on, the Hamilton fauna's EPBA persisted for about 800
thousand years�despite significant fluctuations in relative abundance
of individual bivalve species. Persistence of body-size structure and
the interaction strength between shell-crushing predators and their
bivalve prey suggests long-term stability of food-web structure. This
pattern might at first seem at odds with ecological theory, which
predicts that complex food webs should not persist because of their
inherent instability [3], [40]�[43]. However, a growing number of
studies attribute �flexibility� in food-web structure, arising from
predator behavioral or adaptive switching in prey selection in
response to qualitative and quantitative resource changes (e.g.,
changing prey abundances) in space and time, as a mechanism
contributing to ecological stability (e.g., [42],[44]�[46]). Prey
switching may occur passively due to predator familiarity with an
encountered prey type, or actively as a �choice� made by the predator
to increase fitness [47].
For this mechanism to explain the long-term ecological stability of
the EPBA, Devonian predators would have had to have switched their
feeding patterns, while at the same time maintaining similar predation
pressures on their prey. Our data are consistent with this prediction.
Although average RF throughout the study interval persisted relatively
unchanged, the relative abundance and RF values of individual prey
species are positively correlated (R2 = 0.95), supporting the
prediction that predators did not have rigid feeding patterns.
In modern systems, shell-crushing predator-prey interactions also are
highly size-structured, with predators often larger than their prey
[48], [49]. We assume that this simple body-size relationship applies
to shell-crushing predator-prey interactions in Devonian seas, given
its regularity across habitat types and taxonomic groups in food webs
today [50], [51]. Ecological theory predicts that species persistence
is enhanced with a consistent body-size structure of predators and
their prey (i.e., allometric scaling; [46], [51]), with invertebrate
and vertebrate predators generally on geometric average 10 and 100
times, respectively, larger than their prey [52]. Although we do not
have information on the body sizes of Devonian predators, the lack of
significant change in shell-crushing predation, indexed by RF (and
thus per capita effects of predators on prey), and body-size
distribution of the EPBA, is indirect evidence suggesting that the
predator-prey body size ratio remained high; in other words, most
predators were likely to have been larger than their bivalve prey. If
this general pattern did not hold in the Devonian, we would have
expected change in the EPBA body-size distribution, reflecting new
dynamics of the size-structured predator-prey interaction [53], [54].
Given the effects of adaptive foraging and body size on the
persistence of complex food webs, a possible scenario for ecological
stability of the EPBA emerges. As the size-structured predator-prey
interaction between shell-crushing predators and their bivalve prey
was disturbed by low-level stress (i.e., sea-level change), it is
possible that this disturbance led to fluctuating selection on
interaction strength in space and time and consequently food-web
reconstruction (due to changes in fluctuating abundances of prey). As
environmental conditions changed, different connections in the shell-
crushing predator-prey module of the food web were strengthened
(increasing RF values) while others were dampened (decreasing RF
values). Over time this fluctuating pattern gave the shell-crushing
predator-prey interaction some �flexibility��potential connections
(links) in the food web were turned off or on, while overall
connectance of the module was kept low (i.e., few strong interactions;
[55]) in response to sea-level changes and fluctuations in prey
abundance to enhance EPBA persistence.
Functional redundancy and ecological stability
We have shown that the relative abundance of bivalve species in the
EPBA did not remain stable throughout the depositional cycles of the
Hamilton fauna we sampled; however, at lower levels of resolution
(e.g., presence-absence data) there is evidence that the same bivalve
species were always present. This alternative conclusion is the
consequence of the scale of analysis we used (i.e., the numerical
resolution of the data�a problem that is not fully appreciated; [56]).
Our use of relative abundance data (a high level of resolution),
however, allowed us to detect more subtle changes in the structure of
the EPBA, which had important effects on predator-prey interactions.
Our relative abundance data also suggest a degree of functional
redundancy [57]�[62] or complementarity [63] of the prey species in
the Hamilton fauna EPBA. The functional group we examined consisted of
species with similar, overlapping�but not identical�niches (operating
at the same scale, in the sense of how they experienced the
surrounding environment): sedentary, epifaunal, suspension-feeding
bivalves. We suggest that within-scale, functional overlap of bivalve
taxa may also have contributed to the ecological stability of the
EPBA. As the abundance of one EPBA bivalve species fluctuated (due to
changes in abiotic and/or biotic environmental factors), it was
compensated for�in terms of biomass and energy use�by other species.
Similarly, Ivany ([13]; p. 245) suggested that redundancy �within
nested sets of taxa, such that several taxa proportionately share a
given ecological role and compensate for each others' short-term
abundance fluctuations�� may have contributed to patterns of
ecological stability in fossil assemblages. To our knowledge, our
study is the first to present data supporting this speculation.
If compensatory dynamics have strong stabilizing effects, it is
conceivable that changes in abundance structure of the EPBA may not
have altered properties at the scale of the whole ecosystem. For
instance, theoretical and empirical evidence from modern systems
indicates that ecosystem-level properties, such as productivity,
exhibit less variability in response to environmental change than
changes in abundance of organisms [64], [65]. Conserved body-size
structure (Fig. 4) in the EPBA through time is consistent with this
expectation; in this way, compensatory shifts in species abundance
within the EPBA may have acted as a buffer against diminished
suspension-feeder biomass. We acknowledge the tentative nature of the
evidence regarding this conclusion. A more rigorous test would entail
collecting data on the absolute abundance of species within the EPBA,
which could serve as a proxy for total biomass and energy use. We
suspect, however, that such a test will not change our interpretation,
given that measures of relative and absolute abundance�in organisms as
diverse as trilobites and mammals�are often positively correlated
(i.e., proportional to each other [66]�[68]).
Predators and interaction modules
We assumed that the EPBA interacted with the same group of predators
throughout the study interval. Similarity in shape and position of
repair scars (Fig. 3; [36]) on the shells of bivalve prey supports
this assumption, but is not direct evidence of taxonomic stability in
the composition of the shell-crushing predator functional group. At
present, only lists of possible predators are available [35], [36].
Although we do not know (and may never know) the identity of the
Devonian shell-crushing predators that unsuccessfully attacked bivalve
prey, our results showcase the utility of predation metrics, which
estimate the strength of interaction among a few interacting species
between trophic levels, in tests of long-term ecological stability in
the fossil record. By focusing on a small number of interacting species
�or modules of food webs [37], [39], [69]�it was possible to gain
insight into ecosystem-level processes (e.g., biomass and energy use).
Extending this approach to the EPBA predator-prey module throughout
the remainder of the Hamilton fauna' s duration as well as other
interaction modules (such as symbiosis and competition) is a fruitful
avenue of future research.
Implications for coordinated stasis
Our results have implications for understanding the pattern of
coordinated stasis�long intervals of faunal persistence terminated by
turnover events induced by environmental change [9]. Although
coordinated stasis is a statement about observed patterns of the
fossil record, and not a hypothesis about process, a number of
mechanisms have been proposed to explain the pattern (see [13], for a
review). For instance, ecological locking, in which �ecological
interactions maintain a static adaptive landscape and prevent both the
long-term establishment of exotic species�and evolutionary change of
the native species�� ([70]; p. 11273) and incumbency (i.e., resistance
by incumbents to invading taxa; [13]), have been widely discussed as
possible intrinsic causal mechanisms to explain the pattern of
coordinated stasis (e.g., [13], [70]�[73]). The extrinsic cause of
habitat tracking [74]�[76], in which changes in the physical
environment force organisms to migrate and to track their favored
environments, is another debated [77] mechanism. Although species
migrate individualistically, similar species-specific tolerance
limits, among several taxa, in terms of water depth, substrate type,
and other environmental parameters may give the appearance of groups
of species (essentially biofacies) tracking changes in the physical
environment as a unit [76]. In other words, species distributions
along environmental gradients�especially those related to water depth�
may remain relatively stable, but the species shift spatially as the
gradients themselves shift [11].
We suggest that the energetic set-up of food webs�adaptive foraging of
consumers (e.g., [42]), body-size structure of consumer-resource
relationships (i.e., allometric scaling; [51]), and functional
redundancy of prey species (sensu [57], [58], [78])�offer alternative,
complementary mechanisms to explain coordinated stasis in the fossil
record. We recognize that defining operational criteria for
distinguishing among these alternative mechanisms will be difficult in
most cases because they predict nearly the same behavior. These
mechanisms also are not mutually exclusive. For instance, a low-stress
disturbance (such as sea-level rise) that drives species to migrate
(i.e., habitat tracking, sensu [10]) may result in the relative
abundances of the players changing as the community is reassembled,
but such change, does not necessarily overturn the ecological applecart
�to use Eldredge's [79] apt description�to change the structure and
function of the food web as a whole. In addition, processes may
actually interact additively or synergistically, leading to even a
higher level of ecological stability (e.g., interactive, stabilizing
effects of body-size structure and adaptive foraging in food-webs;
[46]).
Our focus on the internal dynamics of food webs shares with
�ecological locking� (sensu [70]) an emphasis on species interactions.
Ecologic locking �emphasizes the strength and structure of ecological
interactions�in holding ecological relationships relatively constant
so that rank abundances and guild structure do not fluctuate
widely� ([13]; p. 245). This mechanism requires a tight integration of
interacting species (in other words, an �intrinsic� ecological mutual
dependence�the acting, reacting, and co-acting�of EPBA inhabitants,
which essentially �glues� the assemblage together). Our conclusion
that the EPBA food web was stable for about 800 ka, however, does not
imply a �locked� interaction module of shell-crushing predators and
their bivalve prey; that is, a static, highly integrated entity, in
the sense of equilibrium (steady-state) notions of the term [80].
Instead, we view the stable EPBA as an open and flexible food web with
variable species attributes, such as abundance and composition. The
persistence of stable assemblages of interacting organisms is thus
dictated by their capacity to accommodate disturbance�variation and
the capacity to respond rapidly to such variation are critical to the
maintenance of coordination in coordinated stasis.
Paleoecological patterns and minimalist interpretations
Our interpretations assume that the internal dynamics of food webs can
be scaled up to produce predictable patterns in the fossil record. We
adopted a scale-independent view, in which patterns are similar on
multiple scales of observation, although not infinitely (sensu [81]),
because of an increasing body of evidence indicating that biological
processes, such as predation, can act in similar ways across a
spectrum of spatial and temporal scales (see [81]�[83] for reviews).
Our data support this hypothesis. For instance, the positive
correlation we found between the relative abundance of bivalve prey
and RF (an index of predator selectivity)�a pattern evident at a
temporal scale of hundreds of thousands of years�is consistent with
modern examples of prey-switching behavior by predators occurring on
vastly different temporal scales, ranging from days to thousands of
years (e.g., [84], [85]). To the extent that a minimalist
interpretation is adequate, the paleoecological patterns we found are
thus best viewed as local changes summed over vast sweeps of space and
time rather than as the result of �different rules� (i.e., scale-
dependent processes [86] operating at paleontological scales).
Decoupling of ecological patterns
Our study shows that interpretations of ecological patterns of
stability in the fossil record depend on what metrics are used. We
would have rejected the hypothesis of ecological stability if we only
assessed patterns in relative abundance through time. Instead, a
complex pattern of ecological stability emerged when other assemblage-
level properties were taken into consideration. This result raises
serious doubt as to whether the phenomenon can be tested meaningfully
solely based upon the abundance of taxa (which has been the standard
metric used to test for ecological stability in paleoecology; [15],
[19]�[21]). We suggest that multiple lines of evidence are needed to
increase the confidence in the signals derived from paleoecological
data. Our test of ecological stability drew upon different types and
sources of information, requiring the integration of multiple lines of
evidence that converged (and diverged) before conclusions were
reached. Our study thus underscores the critical need for multiple,
comparative datasets in tests of ecological stability in the fossil
record.
Materials and Methods
Sampling
Because it is crucial that all samples represent the same benthic
association, the sampling target for our study consisted of siltstones/
silty mudstones near the �caps� of coarsening upward depositional
cycles or parasequences. The sampled siltstone beds were rapidly
deposited and experienced within habitat time-averaging (sensu [87],
[88]), which excludes the mixing of different depth related
assemblages. Associated specimens are typically well preserved with
little sign of corrasion and fragmentation; thus, the amount of time
in residence on the seafloor was probably rather short (see [26],
[89]). Most siltstones are not associated with evident sediment
starvation, such as phosphatic nodules; however, many shells and most
multi-element skeletons are disarticulated and the sediments are
rather strongly bioturbated (mainly Zoophycos) in some cases
indicating sedimentation rates low enough for fairly thorough
breakdown of primary sediment structures and articulation of
skeletons. Overall, time averaging on the scale of decades to a
maximum of a few hundred years can be assumed for the targeted
siltstone beds.
The majority of epifaunal bivalve specimens found in these siltstone
beds are preserved as internal, external, or compression molds, all of
which yield excellent surface detail. The morphology of these taxa is
also ideal for preserving evidence of predatory attacks by durophagous
(shell-crushing) predators. The pterioid taxa we studied possessed at
least one valve with a simple, exterior prismatic calcite layer that
made their shell highly flexible [90], [91]. This microstructural
trait would have enabled Devonian pterioids to seal their shells
tightly, enabling them to survive a high degree of shell damage
induced by shell-crushing predators ([36]; Fig. 3), as is the case
with modern bivalve groups that possess these traits [92]�[94].
At seven localities (Table 4), we target-sampled bivalve specimens in
the EPBA. Ottens et al. [95] showed, if relatively common taxa are
targeted, and efforts are made to collect all specimens, that targeted
collecting provides results similar to those from bulk collecting.
Outcrop conditions�small road cuts or stream beds�prevented the
collection of replicate taxon-specific ( = targeted) samples, due to a
lack of extensive and continuous exposures of the sampled siltstone
beds to assess any underlying outcrop-scale patchiness [96], [97] of
the EPBA. Taxon-specific sampling, however, tends to average out
spatial variation within a locality [95], because the nature of the
collecting process�searching a circumscribed area of an outcrop for
float specimens�results in the pooling of small numbers of specimens
collected from multiple sites distributed over a large sampling domain
into a single sample. This sampling strategy thus has the same
intrinsic advantage as combining multiple, small bulk samples to
average out patchiness within a locality [97]. All specimens (Table
S4) included in this study have been deposited at the Paleontological
Research Institution (PRI), Ithaca, New York, USA (PRI Accessions 1552
and 1626). No permits were required for the described study, which
complied with all relevant regulations.
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Table 4. Locality list.
doi:10.1371/journal.pone.0063071.t004
Assemblage metrics
Abundance.
A full description of the ecological structure of fossil assemblages
must include information on the abundance distribution of its members
[98], [99]. It is not surprising then that the first tests of
ecological stability in the Hamilton fauna assessed abundance patterns
[19]�[21]. To test for stability in the abundance structure of the
EPBA, we counted and identified all left valves in our samples to at
least the �genus� level based on morphology. Fragments of specimens
were only counted if at least one-third of the left valve was present.
Body size.
Species assemblages are also strongly structured by body size of their
members [100]. Species interactions, metabolic rate, life history and
geographic distribution are all influenced by the body size of
organisms [100], [101]. Therefore, information on the distribution of
body sizes within an assemblage of species is a useful descriptor for
a large amount of biological information reflecting the dynamics and
structure of food webs [102]. To test for stability in body-size
structure of the EPBA, we measured the dorso-ventral length of the
left valve of all complete specimens greater than 5 mm to the nearest
0.05 mm.
Predation.
The structure of an assemblage of species also depends on how species
interact. Top-down forces (i.e., predation) have long been recognized
as important community structuring mechanisms (e.g., [103]). Predators
may affect prey populations directly by preying on them or indirectly
by altering prey traits including behavior, morphology, or habitat use
[39]. Therefore, information on the strength of interactions between
predators and prey is a useful descriptor of patterns of energy use
and structure of the EPBA in the Hamilton fauna. To test for stability
in predation pressure, we traced the history of the interaction
between epifaunal bivalves and their shell-crushing predators. We
focused on this interaction because of the important role epibenthic
shell-crushing predators have in structuring benthic marine
communities in modern systems (e.g., [104], [105]).
We calculated an assemblage-level RF�the number of specimens with at
least one repair scar on the shell [106]�in each of our EPBA samples
as our proxy for predation pressure. Only repair scars identified as
resulting from biotic agents were counted in our tallies. Breakage-
induced shell damage that resulted from unsuccessful attacks by
predators was differentiated from other non-biological taphonomic
processes, such as sediment compaction, by the presence of
characteristic features of damage and repair, including scar position
and geometry (e.g., jagged, scalloped shape; [106]), changes in growth
line banding, and loss or offsetting of minor radial surface
ornamentation, if present (Fig. 3). Following Nagel-Myers et al. [36],
only the left valve of specimens that preserve the outer shell layer
as an external mold or compression steinkern were used in our RF
analysis.
Because RF estimates are sometimes challenging to interpret in terms
of predation pressure (i.e., lethal predation [106]�[109]), we
standardized our data to increase confidence that comparisons were
made between samples with equivalent likelihoods of accumulating
repair scars [106]. We assessed potential for bias in our RF estimates
by checking whether the accumulation of shell repairs was dependent on
the taxon used and/or size of specimens [106], [110]�[113].
Controlling for these factors enhanced our ability to detect
ecologically meaningful signals about predation pressure from RF
estimates [106]. We used an �assemblage-level� approach (sensu [114],
[115]) in calculating RF because our analysis was restricted only to
an assemblage of functionally similar (suspension feeding) bivalve
taxa that share a common adaptive syndrome (e.g., mantle retraction,
shell microstructure, mobility etc.) and mode of life, and not the
entire Hamilton bivalve fauna�which is an amalgam of heterogeneous
signals that is difficult to interpret meaningfully [116], [117].
Data analysis
Three statistical analyses were used to assess change over time. We
used a multinomial model to detect changes in abundance over time, a
generalized linear model to assess any effects of stratigraphic
position (time unit), locality, and taxon identity on body size, and a
logistic regression model to determine effects of time unit, locality,
taxon identity, and body size on RF. We used model ranking techniques
throughout to assess importance and significance of effects.
When presenting model ranking results, we report Akaike Information
Criterion (AIC), Bayesian Information Criterion (BIC), Akaike weights,
and Bayesian weights (see [118] for definitions and comparisons).
There is disagreement about which criterion, AIC or BIC, is better for
assessing model support. AIC is viewed as favoring more complex models
when the real model is more complex than any of the candidate models.
BIC is considered to be more conservative in that it requires more
evidence to overturn a simple model. It also assumes that the correct
model is in the set being considered and each model in the set is a
priori equally likely. Both methods require approximations that are
difficult to assess in practice (for additional paleoecological
applications see [119]�[122]).
For the two regression models, in addition to model ranking results,
we also report diagnostic information. Because model ranking is
appropriate only for plausible models, we ensured reasonable fits by
inspecting residuals and reporting model deviance with respect to the
residual degrees of freedom. If the ratio of deviance to degrees of
freedom is greater than two, there is evidence for defects in the
model (see [123] for details and examples).
All analyses were done in �R� [124]. For additional information on
statistical analyses see Methods S1.
Abundance.
We used the model-ranking methods developed by Handley et al. [125] to
assess whether the abundance structure of the EPBA changed through
time. To compute relative abundances through time, taxon counts for
each were treated as multinomial observations drawn from an underlying
ecological distribution. The optimal model of EPBA structure was
selected from a set of hypotheses about those distributions, based on
information-theoretic measures to assess the model's support from the
data. The models considered included stasis, in which samples from
each time unit share the same underlying sampling distribution,
complete heterogeneity, in which each sample has a different sampling
distribution, and all other ordered groupings of samples by time unit.
Body size.
We applied a generalized linear regression model to test whether
stratigraphic position (time unit), locality, or taxon identity had
any effect on the body-size structure of the EPBA. Body size is a
response variable with time unit, locality, and taxon serving as
categorical covariates. To detect whether different taxa are changing
sizes over time, we also included a model that incorporates
interactions between time unit and taxon (a two-way ANOVA with
interaction terms).
Predation.
To assess whether predation pressure (indexed by RF) in the EPBA
changed through time, we used logistic regression, a technique
commonly used in paleoecology (e.g., [126]). Our repair data represent
binary outcomes (1 = attacked, 0 = not attacked) with covariates
stratigraphic position (time unit), locality, taxon identity, and body
size. We tested if time unit, locality, taxon, or body size has any
effect on RF. To detect whether different taxa had different RFs over
time, we also included a model that incorporates interactions between
taxon and time unit (a two-way ANOVA with interaction terms).
Supporting Information
Methods S1.
Expanded explanation of statistical analyses.
doi:10.1371/journal.pone.0063071.s001
(DOCX)
Table S1.
Relative abundance by taxon and stratigraphic unit.
doi:10.1371/journal.pone.0063071.s002
(XLSX)
Table S2.
Average size of specimens by taxon and stratigraphic unit.
doi:10.1371/journal.pone.0063071.s003
(XLSX)
Table S3.
Repair frequency by taxon and stratigraphic unit.
doi:10.1371/journal.pone.0063071.s004
(XLSX)
Table S4.
Data for all analyzed scarred and unscarred specimens of the EPBA by
locality and taxon.
doi:10.1371/journal.pone.0063071.s005
(XLSX)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063071