The Micropaleoecology Framework: Evaluating Biotic Responses to Global Change Through Paleoproxy, Microfossil, and Ecological Data Integration

Abstract

The microfossil record contains abundant, diverse, and well‐preserved fossils spanning multiple trophic levels from primary producers to apex predators. In addition, microfossils often constitute and are preserved in high abundances alongside continuous high‐resolution geochemical proxy records. These characteristics mean that microfossils can provide valuable context for understanding the modern climate and biodiversity crises by allowing for the interrogation of spatiotemporal scales well beyond what is available in neo‐ecological research. Here, we formalize a research framework of “micropaleoecology,” which builds on a holistic understanding of global change from the environment to ecosystem level. Location: Global. Time period: Neoproterozoic‐Phanerozoic. Taxa studied: Fossilizing organisms/molecules. Our framework seeks to integrate geochemical proxy records with microfossil records and metrics, and draws on mechanistic models and systems‐level statistical analyses to integrate disparate records. Using multiple proxies and mechanistic mathematical frameworks extends analysis beyond traditional correlation‐based studies of paleoecological associations and builds a greater understanding of past ecosystem dynamics. The goal of micropaleoecology is to investigate how environmental changes impact the component and emergent properties of ecosystems through the integration of multi‐trophic level body fossil records (primarily using microfossils, and incorporating additional macrofossil data where possible) with contemporaneous environmental (biogeochemical, geochemical, and sedimentological) records. Micropaleoecology, with its focus on integrating ecological metrics within the context of paleontological records, facilitates a deeper understanding of the response of ecosystems across time and space to better prepare for a future Earth under threat from anthropogenic climate change.

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Ecology and Evolution, 2024; 14:e70470
https://doi.org/10.1002/ece3.70470
Ecology and Evolution
REVIEW ARTICLE OPEN ACCESS
The Micropaleoecology Framework: Evaluating Biotic
Responses to Global Change Through Paleoproxy,
Microfossil, and Ecological Data Integration
AdamWoodhouse1,2 | AnshumanSwain3,4 | JansenA.Smith5 | ElizabethC.Sibert6 | AdrianeR.Lam7 |
JenniferA.Dunne8 | AlexandraAuderset9
1School of Earth Sciences, University of Bristol, Bristol, UK | 2University of Texas Institute for Geophysics, University of Texas at Austin, Austin, Texas,
USA | 3Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA | 4Museum of Comparative Zoology,
Harvard University, Cambridge, Massachusetts, USA | 5Department of Earth and Environmental Sciences, University of Minnesota Duluth, Duluth,
Minnesota, USA | 6Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA | 7Department of
Earth Sciences, Binghamton University, Binghamton, New York, USA | 8Santa Fe Institute, Santa Fe, New Mexico, USA | 9School of Ocean and Earth
Science, University of Southampton, Southampton, UK
Correspondence: Adam Woodhouse (adam.woodhouse@bristol.ac.uk)
Received: 25 July 2024 | Revised: 1 October 202 4 | Accepted: 3 October 2024
Funding: This work was supported by Santa Fe Institute.
Keywords: biogeochemistry| biomarkers| climate change| conservation paleobiolog y| ecosystems| IODP| microfossils| oceanography|
paleoceanography| paleontology
ABSTRACT
The microfossil record contains abundant, diverse, and well- preserved fossils spanning multiple trophic levels from primary
producers to apex predators. In addition, microfossils often constitute and are preserved in high abundances alongside contin-
uous high- resolution geochemical proxy records. These characteristics mean that microfossils can provide valuable context for
understanding the modern climate and biodiversity crises by allowing for the interrogation of spatiotemporal scales well beyond
what is available in neo- ecological research. Here, we formalize a research framework of “micropaleoecology,” which builds on a
holistic understanding of global change from the environment to ecosystem level. Location: Global. Time period: Neoproterozoic-
Phanerozoic. Taxa studied: Fossilizing organisms/molecules. Our framework seeks to integrate geochemical proxy records with
microfossil records and metrics, and draws on mechanistic models and systems- level statistical analyses to integrate disparate re-
cords. Using multiple proxies and mechanistic mathematical frameworks extends analysis beyond traditional correlation- based
studies of paleoecological associations and builds a greater understanding of past ecosystem dynamics. The goal of micropal-
eoecology is to investigate how environmental changes impact the component and emergent properties of ecosystems through
the integration of multi- trophic level body fossil records (primarily using microfossils, and incorporating additional macrofos-
sil data where possible) with contemporaneous environmental (biogeochemical, geochemical, and sedimentological) records.
Micropaleoecology, with its focus on integrating ecological metrics within the context of paleontological records, facilitates a
deeper understanding of the response of ecosystems across time and space to better prepare for a future Earth under threat from
anthropogenic climate change.
This is a n open access ar ticle under the terms of t he Creative Commons Attr ibution License, which p ermits use, dis tribution and repro duction in any medium, p rovided the orig inal work is
properly cited.
© 2024 T he Author(s). Ecology and Evolution publis hed by John Wiley & Sons L td.

2 of 11 Ecology and Evolution, 2024
1 | Introduction
One of the great societal challenges of the 21st century is adapt-
ing to and mitigating the consequences of anthropogenic cli-
mate change. Extreme, rapid change driven by anthropogenic
activities impacts both the environment (e.g., CO2- induced
global warming, changes in nutrient distributions) and eco-
systems (e.g., biodiversity loss due to over- fishing and hunting,
land- use changes). The impacts of specific climate forcing on
individual species, as well as feedbacks between environmen-
tal and biological changes at different scales, can have major
add- on effects on the structure and function of natural systems
that can push ecosystems past tipping points, leading to abrupt
shifts to contrasting ecosystem states (Dakos etal. 2019) and,
in some cases, wholesale ecological collapse (Brook, Sodhi,
and Bradshaw2008). These cascading changes not only impact
the constituent organisms and their interactions but also the
broader- scale ecosystem functions and services that are vital re-
sources for human existence (IPBES2019).
Teasing out the impacts of environmental change on ecosystem
dynamics is a complex problem that requires interdisciplinary
solutions and the best available data. Ecosystems function at
multiple spatial and temporal scales with interacting biotic and
abiotic components. Although the records of these dynamics are
variable in availability and quality, they are essential for con-
structing a comprehensive understanding of how past, present,
and future versions of the Earth system function under different
climate regimes.
Here, we develop a framework for investigating climate-
ecosystem dynamics throughout the geological record that
explicitly leverages microfossil data. This framework, which
we call “micropaleoecology,” unites the exceptional quality
and coverage of multi- trophic level micropaleontological re-
cords with geochemical paleo- proxy climatic reconstructions
using neo- ecological metrics (e.g., Hill numbers (Hill 1973),
co- occurrence (Morales- Castilla etal. 2015)) and systems- level
methods (e.g., network- based methods (Bascompte 2007) and
agent- based models (Grimm 1999)). The potential value of the
micropaleoecology framework lies in the ability to investigate
ecosystem- wide changes, from primary producers to consumers
across all trophic levels, in relation to past environmental shifts.
The high temporal and spatial resolution and coverage of the
microfossil and biogeochemical records, combined with abiotic
environmental datasets, provides a holistic approach to infer
linkages between ecosystems and external forcing mechanisms.
This interdisciplinary research framework can contribute to the
understanding of ecosystem sensitivity and the potential im-
pacts of environmental and biological change (Hunt, Cronin,
and Roy2005; Yasuhara etal.2012, 2017a, 2017b, 2020a, 2020b;
Moffitt etal.2015; Chiu etal.2 017; Cramer etal.2017; Myhre
etal.2017; Schmidt2018; Doi, Yasuhara, and Ushio2021).
2 | Records of Biotic and Abiotic Change
Many datasets focus on restricted data types (e.g., biotic or
abiotic; neontological or paleontological; taxon- specific rather
than community- based), perpetuating challenges for develop-
ing a long- term, ecosystem- wide perspective. For example, the
extent of long- term ecological studies is largely confined to the
last 50 years (Dornelas etal.2018), with an average study win-
dow of 3–5 years (Estes et al.2018) and sampling intervals of
days, weeks, or months. However, despite the accelerated rate
and magnitude of the current climate crisis in comparison with
geological crises, many “modes” of variability in modern ecosys-
tems are decadal or longer in scale and not captured with these
short time series (e.g., Dietl etal.2015; Mantua and Hare2002;
Eguchi etal. 1999, 2003; Gupta etal. 2002; Hull, Darroch, and
Erwin2015; Tsutsui etal. 2016). The patterns detected in these
modern studies provide a snapshot of ecosystems that is valu-
able in its own right but many “unsolved problems in ecology”
(see Dobson, Tilman, and Holt 2020) require broader spatial
and deeper temporal perspectives that can be gained by viewing
these short- term trajectories within the scope of the longer pro-
cesses of which they are a part (Dietl etal.2015; Lazarus1994).
Moreover, the majority of modern observations began within
a climate system already altered by anthropogenic forcing
(McCulloch et al. 2024), highlighting the need for biological
datasets that effectively capture background states and variabil-
ity before system perturbations.
One of the best resources for interrogating the long- term relation-
ship between life and the environment is the microfossil record.
Microfossils—defined here as fossils requiring the use of a mi-
croscope for study—provide broad geographic coverage through
space and time (Armstrong and Brasier 2013). Microfossils en-
compass nearly all trophic levels, from primary producers (e.g.,
diatoms, calcareous nannofossils/coccolithophores, pollen) to top
predators (e.g., fish teeth, shark dermal denticles, mammal teeth),
and many groups in bet ween (e.g., foraminifera, ost racodes, fu ngi).
The high preservation potential of microfossils allows them to be
collected, sometimes in great numbers, from outcrop sections
and sediment cores from ocean and lake environments, in many
cases at high temporal resolution due to their nearly uninter-
rupted deposition in aquatic basins (Figure1; see BioDeepTime,
Smith etal.2023a; Smith etal.2023b; Marsaglia etal.2015; IODP
Science Support Office, 2018). Such excellent spatiotemporal
coverage has led to microfossil- based studies addressing ques-
tions about evolutionary rates, biodiversity hotspots, and biogeo-
graphic patterns with temporal durations ranging from seasonal
to multi- million year, on temporal scales from the Precambrian
to Recent, and on geographic scales from local to global (e.g., de
Vernal and Hillaire- Marcel 2008; Alvarez etal. 2019; Trubovitz
etal. 2020; Pilarczyk etal.2014; Lam and Leckie2020; Lowery
et al. 2020; Yasuhara et al. 2017a , 2017b, 2020a, 2020b, 2022;
Nowak, Schneebeli- Hermann, and Kustatscher 2019; Jamson,
Moon, and Fraass2022; Song etal.2011; Lower y and Fraass2019;
Schopf 1993; Riedman et al. 2014; Fenton et al. 2016a , 2016b,
2023; Jonkers etal. 2019; Sibert etal. 2018; Sibert and Rubin 2021;
Mottl etal. 2021; Woodhouse etal.2023b; Woodhouse etal.2021,
2023a; Swain, Woodhouse etal.2024; Aze etal. 2011).
Large paleontological datasets (e.g., GBDB (Fan etal. 2013),
Neotoma (Williams et al. 2018), Neptune (Renaudie et al.
2020), DINOSTRAT (Bijl 2022), Paleobiology Database (Uhen
etal. 2023), and Triton (Fenton, Woodhouse etal. 2021)) are
invaluable resources for evaluating past global biodiversity
change and can be used to assess ecological and evolution-
ary features of past climate and environmental perturbations,
such as size selectivity during extinctions (Rego etal.2012),

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biogeographic range shifts (Fenton et al. 2023; Woodhouse
et al. 2023a), and changes in trophic dynamics (Smith
etal. 2022; Woodhouse et al. 2023b; Swain 2023). However,
not all data in these large accumulations lend themselves to
high- resolution, multi- trophic- level ecological reconstruction.
For example, the macrofossil record occasionally offers high
species richness, large abundances, and exceptional preser-
vation, supporting important insights into ancient ecosys-
tems (e.g., Dunne etal. 2014), but such records are very much
the exception, often occurring in geographically isolated
lagerstätte (Benton 1989; Kidwell and Flessa 1995; Benton
etal.2011; Cisneros etal. 2022). Indeed, compared to micro-
fossils, macrofossils tend to have small population sizes, low
preservation potential, and are primarily preserved in tran-
sient depositional environments with irregular occurrences in
Earth's history (e.g., Benton1989; Benton etal.2011).
Complementary to the microfossil record, organic “molecular”
fossils, including biomarkers and ancient DNA, can provide
more information on some fossil organisms (e.g.,
UK37′
from
coccolithophores) as well as direct evidence of organisms with
soft anatomies that are unlikely to fossilize (e.g., picoeukary-
otes). These non- fossilizing organisms play a fundamental role
in marine ecosystems through photosynthesis and recycling of
organic matter. Molecular fossils allow for high- resolution bio-
logic, paleoceanographic, and paleoclimatic analyses, and are
broadly applicable to various aquatic and terrestrial environ-
ments (e.g., Sepúlveda etal. 2009; Lupien etal. 2022; Cluett etal.
2023), and ancient DNA analyses can provide comprehensive
data on ancient terrestrial and marine community dynamics
on multi- million year timescales in exceptional circumstances
(Kuwae et al. 2020; Armbrecht et al. 2022; Kjær et al. 2022;
Nakamura et al. 2023). Molecular fossils can be used to re-
construct past sea surface temperatures (e.g., GDGTs/ TEX86,
Schouten etal. 2002), oxygen conditions in the water column and
sediment (e.g., pristane/phytane ratio or bulk sedimentary ni-
trogen isotopes, Rontani etal. 2003; Altabet and Francois1994),
or heterotrophic vs. autotrophic carbon cycling type (Figure 2;
also see list of biomarkers in Volkman etal. 1998). These fos-
sils are especially useful in reconstructing spatial and temporal
nutrient availability, including essential nutrients like nitrogen
and phosphorus (Redfield1958), which ultimately drive ecosys-
tem productivity and the overarching structure of microfossil
communities (e.g., alkenones and chlorins, Harris et al.1996;
Raja and Rosell- Melé 2021). Furthermore, there are dozens of
non- skeletal, sediment- bound inorganic proxies that preserve
records of environmental conditions (e.g., X- ray fluorescence
(Croudace and Rothwell 2015), and natural gamma radiation
(Adams and Gasparini 1970)).
A wide array of geochemical proxies derived from microfossils,
molecular fossils, and bulk sediments (TableS1; Figure2) have
additionally been developed to study climate- ecosystem interac-
tions through further elucidation of paleoclimatic/paleoceano-
graphic (e.g., temperature and CO2), paleoenvironmental (e.g.,
nutrient and oxygen concentrations), and paleoecological (e.g.,
biogenic barium) conditions. Such records have unveiled the
changing nature of Earth's ice volume and temperature through
the Cenozoic (e.g., Zachos etal.2001, 2008; Cramer etal. 2009,
2011; Westerhold et al. 2020), Mesozoic (e.g., Trotter et al.
FIGUR E  | Geographical occurrence records of (A) marine macrofossils (from Paleobiology Database) and (B) microfossils (combined records
from BioDeepTime, Triton and Sibert etal. 2014, 2016, 2020 and unpublished data). (C) and (D) show the same records on a paleolatitudinal- time a xis
of 1- million- year time bins and 5° paleolatitudinal bands.
Paleocene Eocene Oligocene Miocene Pli. Pl.
Paleogene Neogene Q
0
10
20
30405060
Age (Ma)
0
15
30
45
60
75
90
–
15
–
30
–
45
–
60
–
75
048
Paleocene Eocene Oligocene Miocene Pli. Pl.
Paleogene Neogene Q
0
10
20
30405060
Age (Ma)
0
15
30
45
60
75
90
–
15
–
30
–
45
–
60
–
75
Number of occurrence records
(in logarithmic scale)
AB
CD
Paleolatitude
Macrofossils Microfossils

4 of 11 Ecology and Evolution, 2024
2015; Huber etal.2018), and Paleozoic (e.g., Trotter etal. 2008;
Quinton etal. 2018). Records of oceanic conditions have been
reconstructed from geochemical proxies, such as pH estimated
from B/Ca ratios in planktic foraminifera (e.g., Sanyal et al.
1995; Yu etal. 2007; Foster and Rae 2016), past ocean circulation
as estimated from neodymium isotopes preserved in fish teeth
(e.g., Martin and Haley 2000; Dera etal. 2009; Huck etal. 2016;
Thomas etal. 2014; Kender etal. 2018), and primary productivity
from nitrogen isotopes obtained from a menagerie of microfos-
sils or bulk sediment (e.g., Sigman etal. 1999) (Figure2). Such
records of abiotic system changes are informative in their own
right, and have prov ided insight into the patterns of Antarctic ice
growth and decay (e.g., Patterson etal. 2014), surface ocean cir-
culation shifts (e.g., Lam etal.2021); and atmospheric changes
(e.g., Groeneveld etal. 2017), highlighting how such systems re-
spond to times of increased atmospheric CO2 concentrations a nd
global warmth. In addition, results from climate and ocean mod-
els can add another dimension to the analyses when combined
with fossil studies (e.g., Lam, Stigall, and Matzke 2018; Lam,
Sheffield, and Matzke2021). The microfossil and molecular fos-
sil record becomes even more informative when integrated with
such environmental and geochemical proxy records through in-
novative usage of system- level analytical methods (e.g., network
analyses, dynamical system models, etc.). Such syntheses can
elucidate biotic and abiotic changes over durations that encapsu-
late the complex and long- acting processes at work within eco-
systems (e.g., de Vernal and Hillaire- Marcel 2008; Westerhold
etal.2020; Mottl etal. 2021; Woodhouse etal.2022; Hou etal.
2023; Sepúlveda etal. 2009).
Traditionally, work on geochemical, paleoclimatic, and paleoen-
vironmental reconstructions has operated independently from
ecological and evolutionary questions, despite the same physical
samples being used and complementary data being produced.
Integration of paleontological and geochemical datasets is crit-
ical to developing a more comprehensive understanding of the
ecological responses to environmental change. Global efforts
to investigate the rich geochemical environmental proxy and
microfossil datasets are facilitated by the 55+ year legacy of
scientific ocean drilling, which provides an excellent founda-
tion of exceptional spatiotemporal scale on which to build an
ecosystem- wide view of life's interactions with environmental
changes—in short, the perfect place to explore the micropaleo-
ecology framework.
3 | Micropaleoecology, a Synthesis of Perspectives
The goal of the micropaleoecology framework is to investi-
gate how environmental changes impact the component and
FIGUR E  | Legend on next page.
assemblage
trace elements*
trace elements*
bioactive element ratios**
trace elements*
trace elements*
FIGUR E  | A dominantly marine- based selection of (bio)
geochemical & ecological proxies and their respective archives to
reconstruct various environmental parameters. Dark purple fields
indicate existing studies (see Supporting Information for specific
references), light purple fields indicate potential measurements based
on the geochemical proxy which can be applied to different archives in
the future, grey fields indicate no application so far. * = e.g., Na/Ca, Mg/
Ca, Sr/Ca etc., ** = e.g., Ca/Cd, Ca/Ba, Ca/Zn.

5 of 11
emergent properties of ecosystems through the integration of
multi- trophic level body fossil records (primarily using mi-
crofossils, though incorporating macrofossils where possible)
(Figure 1) with contemporaneous molecular, geochemical,
and sedimentological records across local and global scales
(Figure 2). Concomitant analyses of data from each of these
sources in a framework motivated by modern ecological and
Earth system concepts will enable a more comprehensive view
of Earth's ecosystem dynamics, particularly when also har-
nessing advances in big data collation and high- performance
computing.
By defining the framework of micropaleoecology, we seek to
form a nucleus of theory and methodology that brings together
ideas and researchers working in similar but often siloed dis-
ciplines. Similar interdisciplinary syntheses have grown in the
past decade. For example, conser vation paleobiology has brought
together paleontologists and conservation biologists working on
conservation issues (Dietl et al.2015; Dillon et al. 2022), and
archaeoecology provides an intellectual home for ecologists,
archaeologists, and paleontologists seeking to understand the
impact of humans on ecosystems since our species evolved
(Crabtree and Dunne 2023). Similarly, micropaleoecology brings
together micropaleontologists, (bio)geochemists, oceanogra-
phers, ecologists, and paleontologists (to name a few) working
to disentangle the complex interactions between organisms and
the environment. Although not defined formally, research that
we would consider micropaleoecology has been ongoing, even if
not previously named as such (e.g., Hunt, Cronin, and Roy2005;
Yasuhara etal.2012; Moffitt etal.2015; Chiu etal.2017; Cramer
etal.2 017; Myhre etal.2017; Doi, Yasuhara, and Ushio2021),
and the term “micropaleoecology” has occasionally appeared in
the literature, where it was passingly—and convergently—used
to describe the intersectionality of microorganisms and environ-
ment (e.g., Wignall 1990; Elicki 2006; Diz etal. 2018; Hebda etal.
2022). An interdisciplinary approach that cross- cuts traditional
research boundaries will unlock and unite existing literature
and datasets to more comprehensively investigate the interplay
among the multiple climatic, environmental, and biological
variables shaping the Earth and its ecosystems through time.
To date, there is a dearth of studies that combine biotic with abi-
otic records to fully capture and investigate the intricacies of the
Earth system. Prior efforts by biologists and paleontologists have
created biological- focused databases to synthesize disparate
neontological and paleontological datasets (e.g., Lazarus1994;
Fenton, Woodhouse et al. 2021; Williams et al. 2018; Bijl
2022; Smith etal.2023a; Smith etal.2023b; Sessa etal.2023).
Similarly, working groups composed of (paleo)oceanographers,
paleoclimatologists, geochemists, Earth systems modelers, and
sedimentologists have worked to synthesize records of abiotic
changes, often with a focus on improving climate models (e.g.,
Haywood etal.2011; Judd etal. 2022). Although many individ-
ual biotic and abiotic records are available from data aggrega-
tors (e.g., PANGAEA, Diepenbroek etal. 2002), there is a lack of
standardization or ability to aggregate and collate these dispa-
rate datasets easily, but some efforts have been made (e.g., Sessa
etal.2023).
To compile and aggregate such disparate databases, harmoniza-
tion across metrics and fields is essential; however, this process
is complicated by many idiosyncrasies of the data sources, in-
cluding challenges relating to nomenclature, age models, da-
tabase structure, and communication. For use in taxon- based
ecological analyses, maintaining and monitoring synonymiza-
tion of taxonomy across timescales and regions is a critical step
for the collation of data from different time periods, geographic
regions, and disciplines (e.g., Mottl etal. 2021). Reporting how
age models are developed, along with raw data, precise sample
depths and localities, and associated datum age and depth un-
certainties, are essential for linking the different types of data
(e.g., biological, environmental, geochemical). Standardization
and homogenization of biotic and abiotic database structures
require cross- talk between experts to establish common ter-
minology, methods, and quality standards (e.g., sample resolu-
tion, age model quality), synonymize database field names, and
build database structures that can accommodate the nuances
inherent to each data type. We share an example of such an in-
terdisciplinary synonymized database structure that is able to
accommodate both paleoceanographic and paleontological data
in an integrated way (see Supporting Information). Lastly, to re-
alize the full potential of such a comprehensive database and
gain insights across timescales throughout Earth history, in-
creased discussions and collaborations must take place between
researchers interested in geo- and ecological sciences including,
but not limited to geochronology, paleobiology, paleoclimate,
paleoceanography, and ecology.
4 | Building the Micropaleoecology Framework
The concept of integrating fossil records with environmental
change dates back centuries (e.g., Parkinson 1822). The micro-
paleoecology framework builds on this concept from the organ-
ism to ecosy stem level, by integrati ng geochemical proxy records
with (micro)fossil records and metrics, drawing on mechanistic
and systems- level statistical analyses to link between the re-
cords. Although it is impossible to reconstruct every aspect of
an ancient ecosystem, the integration of organism groups across
multiple trophic levels (including less commonly used fos-
sils like fish otoliths, ichtyoliths, ostracods, and bacteria) with
multiple paleoproxies simultaneously allows for multi- variate
deconstruction of drivers of environmental, ecological, and evo-
lutionary change: a true ecological view of past ecosystems.
Even though the micropaleoecology framework has not yet
been applied in full form, its basic ideas and methods have
been used in previous studies (see Figure 3). Notable examples
include the work of Britten and Sibert (2020), who provided an
organism group- specific example of a multi- metric, systems-
based approach investigating mechanistic drivers of high fish
abundance during the Early Eocene Climate Optimum by inte-
grating paleo- temperature records and within- assemblage fish
tooth size distributions. To do so, they applied a size- structured
trophic transfer model and determined that elevated fish abun-
dance during this interval was driven by increases in trophic
transfer efficiency in pelagic marine ecosystems with extreme
warmth (Britten and Sibert 2020).
Lam, Sheffield, and Matzke (2021) implemented
phylogenetically- informed paleobiogeographic analyses to
infer disper sal paths and speciation t ypes across t he Ordovician

6 of 11 Ecology and Evolution, 2024
for the diploporan echinoderms. Using biogeographic stochas-
tic mapping, they inferred that founder- event speciation was
critical to the evolution of the group through time, and that
dispersal between Baltica and the mid- continent of Laurentia
became more prevalent from the early to late Ordovician. A
lack of correlation among speciation events, sea level, atmo-
spheric oxygen levels, temperature, and carbon cycle changes
indicate diploporans were responding to additional abiotic
processes. Although this study focused on macrofossils, it ex-
emplifies the type of research we advocate for in the micropal-
eoecology framework and the potential beneficial inclusion of
additional information from the fossil record (e.g., macrofos-
sils), when possible.
Woodhouse et al. (2023b) demonstrated the application of a
network- based approach that can be used to good effect in the
micropaleoecology framework. They used this approach to an-
alyze a dataset of planktic foraminifera with a high spatiotem-
poral resolution and identified co- occurrence and specialization
patterns of foraminiferal species in the last ~15 million years
through a lens of trait- based ecology and morphology. The re-
sults demonstrated that in planktic foraminifera, even though
the latitudinal biodiversity gradient has remained invariant
for the past 15 million years (i.e., tropics and near- tropics are
species- rich), the areas where most ecological niches coexisted
equitably have changed drastically across climatic conditions
(Woodhouse etal.2023b).
Moretti et al. (2024) integrated geochemical proxy records
(nitrogen isotopes, sea surface temperature) with microfossil
records (planktic and benthic foraminifera body size) to un-
derstand environmental and ecological changes during the
Paleocene- Eocene Thermal Maximum (PETM). They used
these data to infer changes in oxygen levels in the tropical
North Pacific and how these changes affected foraminifera
body size. The study hints at the role of oxygenation in main-
taining marine habitability amidst climate stress. Although
deep- sea organisms faced extinction during the PETM, those
near the surface were less affected, leaving the possibility that
oxygen played a role in preventing a mass extinction in the
pelagic ecosystems.
These examples, as with the majority of microfossil- based pa-
leoecological studies, focus on the records of one taxonomic
group and its relation to limited paleoclimate variables. In
this area, the micropaleoecology framework can draw from
approaches used in macrofossil- based and modern ecological
studies. Although such studies are often significantly limited
in temporal resolution, they have leveraged cross- taxa ecolog-
ical and network metrics to provide insights into temporally
restricted snapshots of communities (e.g., Sidor etal. 2013;
Smith etal.2022).
The true power of micropaleoecology lies in combining the
strengths of these approaches: leveraging the high volumes of
FIGUR E  | An overview of the proposed micropaleoecology framework with example case studies. An ideal micropaleoecology study includes
data from multiple ta xonomic groups and biogeochemical dat a, evaluated in an a nalytical fr amework informed by ecolog ical theory with mech anistic
models or systems- level statistical analyses. AE, analysis element; PE, primary element; SE, secondary element.

7 of 11
the microfossil record with metrics more commonly applied in
studies of macrofossil communities and modern ecosystems with
broader taxonomic coverage. Additional insights will come from
systematically synthesizing across multiple fossil groups (includ-
ing macrofossils, when possible), combining paleoproxies, and in-
corporating them into an ecosystem- wide framework. Where past
research has incorporated some aspects of the micropaleoecology
framework into their pipelines, integrating all the aspects together
will provide a more complete picture of paleoecological settings.
5 | Conclusions and Future Directions
The micropaleoecology framework can facilitate investigations
of ecosystem changes across multiple trophic levels and spatio-
temporal scales while accounting for environmental factors.
Micropaleoecology, like other emergent interdisciplinary sub-
fields (e.g., archaeoecology, conservation paleobiology), brings
together complementary data, expertises, and perspectives and
can provide a common core of terminology, analyses, and think-
ing to grow connections between researchers. Through the inte-
gration of the detailed resolution and extensive spatiotemporal
coverage of microfossil and (bio)geochemical records, we can
further our understanding of variability, ecosystem resilience,
and the potential ramifications of environmental and biological
shifts. By incorporating ecological metrics into paleontological
and abiotic records, micropaleoecology facilitates a deeper com-
prehension of ecosystem responses over time and space, aiding
in the preparation for a future Earth facing threats from anthro-
pogenic climate change.
Author Contributions
Adam Woodhouse: writing – original draft (equal). Anshuman
Swain: writing – original draft (equal). Jansen A. Smith: writing –
original draft (equal). Elizabeth C. Sibert: writing – original draft
(equa l). Adriane R. Lam: writing – original draft (equal). Jennifer A.
Dunne: w riting – original draft (equal). Alexandra Auderset: w riting
– original draft (equal).
Acknowledgments
All authors contributed equally to this manuscript. We would like to
sincerely thank the staff and scientists who have participated in the
International Ocean Discovery Program and predecessor program legs
and expeditions. Without their contributions, such abundant and rich
data to infer Earth's past climates and ecosystems would not be possi-
ble. This work was made possible through a Workshop grant from the
Santa Fe Institute, and funded by the University of Bristol.
Conflicts of Interest
The authors declare no conflicts of interest.
Data Availability Statement
All data and code to replicate this study are available at htt p s:// github.
com/ anshu man21 111/ micro paleo ecology.
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Supporting Information
Additional supporting information can be found online in the
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