Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic

Abstract

Active coral restoration typically involves two interventions: crossing gametes to facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is to establish self‐sustaining, sexually reproducing coral populations that have sufficient genetic and phenotypic variation to adapt to changing environments. Here, we provide concrete guidelines to help restoration practitioners meet this goal for most Caribbean species of interest. To enable the persistence of coral populations exposed to severe selection pressure from many stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing three to four genets per reef along environmental gradients should be sufficient to capture a majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with one or more phenotypic traits that are predicted to be valuable in the future, such as low partial mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious disease resilience, and high sexual reproductive output. Some effort should also be reserved for underperforming genets because colonies that grow poorly in nurseries sometimes thrive once returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants should be clustered in groups of four to six genets to enable successful fertilization upon maturation. Current evidence indicates that translocating genets among distant reefs is unlikely to be problematic from a population genetic perspective but will likely provide substantial adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices only raise first‐generation offspring. Thus, proceeding with the proposed management strategies even in the absence of a detailed population genetic analysis of the focal species at sites targeted for restoration is the best course of action. These basic guidelines should help maximize the adaptive potential of reef‐building corals facing a rapidly changing environment.

Full text

Considerations for maximizing the adaptive potential of restored
coral populations in the western Atlantic
ILIANA B. BAUMS ,
1,10
ANDREW C. BAKER,
2
SARAH W. D AVIES,
3
ANDR

EA G. GROTTOLI ,
4
CARLY D. KENKEL,
5
SHEILA A. KITCHEN,
1
ILSA B. KUFFNER ,
6
TODD C. LAJEUNESSE,
1
MIKHAIL V. M ATZ,
7
MARGARET W. M ILLER,
8
JOHN E. PARKINSON ,
8,9
AND ANDREW A. SHANTZ
1
1
Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16803 USA
2
Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami,
Florida, 33149 USA
3
Department of Biology, Boston University, Boston, Massachusetts, 02215 USA
4
School of Earth Sciences, Ohio State University, Columbus, Ohio, 43210 USA
5
Department of Biological Sciences, University of Southern California, Los Angeles, California, 90007 USA
6
U.S. Geological Survey, 600 4th Street S., St. Petersburg, Florida, 33701 USA
7
Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712 USA
8
SECORE International, Miami, Florida, 33145 USA
9
Department of Integrative Biology, University of South Florida, Tampa, Florida 33620 USA
Citation: Baums, I. B., A. C. Baker, S. W. Davies, A. G. Grottoli, C. D. Kenkel, S. A. Kitchen,
I. B. Kuffner, T. C. LaJeunesse, M. V. Matz, M. W. Miller, J. E. Parkinson, and A. A. Shantz.
2019. Considerations for maximizing the adaptive potential of restored coral populations in
the western Atlantic. Ecological Applications 29(8):e01978. 10.1002/eap.1978
Abstract. Active coral restoration typically involves two interventions: crossing gametes to
facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies
to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is
to establish self-sustaining, sexually reproducing coral populations that have sufficient genetic
and phenotypic variation to adapt to changing environments. Here, we provide concrete guide-
lines to help restoration practitioners meet this goal for most Caribbean species of interest. To
enable the persistence of coral populations exposed to severe selection pressure from many
stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should
be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing
three to four genets per reef along environmental gradients should be sufficient to capture a
majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with
one or more phenotypic traits that are predicted to be valuable in the future, such as low partial
mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious
disease resilience, and high sexual reproductive output. Some effort should also be reserved for
underperforming genets because colonies that grow poorly in nurseries sometimes thrive once
returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants
should be clustered in groups of four to six genets to enable successful fertilization upon matu-
ration. Current evidence indicates that translocating genets among distant reefs is unlikely to
be problematic from a population genetic perspective but will likely provide substantial
adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices
only raise first-generation offspring. Thus, proceeding with the proposed management strate-
gies even in the absence of a detailed population genetic analysis of the focal species at sites
targeted for restoration is the best course of action. These basic guidelines should help maxi-
mize the adaptive potential of reef-building corals facing a rapidly changing environment.
Key words: adaptive potential; assisted gene flow; biomarkers; coral restoration; genetic diversity;
inbreeding; outbreeding; phenotypic resilience; population enhancement; species selection; unintended selection.
INTRODUCTION
Coral reef ecosystems face unparalleled destruction
due to anthropogenic climate change (McClenachan
et al. 2017, Hughes et al. 2018), and protective coping
mechanisms observed in extant coral populations may
be overwhelmed by the rate of ocean temperature change
(Ainsworth et al. 2016). Thus, the recovery of reef
ecosystems hinges on immediate and decisive actions to
reduce CO
2
emissions globally. Meanwhile, large invest-
ments in coral reef restoration and the population
enhancement of critical reef-building species have been
made in an effort to revive coral communities and main-
tain some ecosystem function and services (Ladd et al.
Manuscript received 25 March 2019; revised 13 June 2019;
accepted 21 June 2019. Corresponding Editor:

Eva Elizabeth
Plaganyi.
10
E-mail: baums@psu.edu
Ecological Applications, 29(8), 2019, e01978
©2019 The Authors. Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any
medium, provided the original work is properly cited.
Article e01978; page 1

2018). Technologies such as artificial selection or genetic
engineering are being contemplated to “design”coral pop-
ulations capable of withstanding current and future envi-
ronmental challenges. However, field applications of these
technologies are not yet ready (van Oppen et al. 2015,
Torda et al. 2017, Cleves et al. 2018). Challenges include
our rudimentary understanding of the genetic basis of
traits that will be essential in the future and limited
knowledge of their interactions (i.e., trade-offs; Muller
et al. 2018), as well as logistical difficulties of propagating
and outplanting engineered corals at ecologically signifi-
cant scales. Protocols for assessing the risks associated
with such interventions are being developed but have yet
to be widely adopted (Baums 2008, IUCN/SSC 2013).
We contend that currently the best approach to
improve reef resilience via direct, restoration-focused
intervention is to harness and foster the adaptive genetic
diversity that is already present in coral populations while
efforts to reduce greenhouse gas emissions continue
(Kleypas et al. 2016, Bay et al. 2017, Matz et al. 2018).
Every coral species exists across a variety of environmen-
tal gradients, some of which occur over small spatial
scales (e.g., fore, back, and patch reefs) while others occur
over very large ones (e.g., across ocean-basins). There is
mounting evidence that corals genetically adapt to their
local conditions (Polato et al. 2010, Barshis et al. 2013,
Kenkel et al. 2013, Dixon et al. 2015), so each species is
in fact a system of sub-populations adapted to diverse
environments and connected by larval migration. In
linked sets of metapopulations, global change could be
rapidly matched by the recombination of pre-existing
adaptive genetic variants, i.e., adaptation based on stand-
ing genetic variation (Hermisson and Pennings 2005,
Baums 2008, Whiteley et al. 2015). Increasingly severe
and frequent mortality events have already led to wide-
spread and continued loss of coral cover (Eakin et al.
2010, Smith et al. 2013, Precht et al. 2016, Walton et al.
2018) and exerted strong selection pressure on these
metapopulations. Therefore, adaptation is likely to be
rapid: survivors of high mortality events are particularly
robust and may be expected to eventually spawn a new
generation of better-adapted corals (Libro and Vollmer
2016, Muller et al. 2018). However, reduced connectivity
between these metapopulations, lower fertilization rates
because colonies are spread further apart (i.e., allee
effects; Knowlton 2001), and universally declining envi-
ronmental conditions across most reef sites reduce the
realization of this potential. If local genetic variation can
be maintained, environmental conditions can be stabi-
lized, and genetic exchange among populations can con-
tinue unimpeded, adaptation may allow corals to keep
pace with climate change for the next 100 years or longer
(Matz et al. 2018). In this context, many interventions are
available now that can help maintain high local genetic
variation and continued exchange among populations.
From this evolution-centric perspective, the goal of
restoration is to establish self-sustaining, sexually repro-
ducing coral populations thereby promoting continuous
genetic adaptation of the species, both locally and
throughout its range. This approach is congruent with
endangered species recovery goals and aligned with but
distinct from some current restoration guidelines
focused on ecological goals such as coral cover or habi-
tat provision. Measuring success using these metrics by
themselves may be insufficient to ensure the long-term
future of restored corals, as ecological success may only
be temporary in the absence of self-sustaining coral pop-
ulations. Instead, our focus is on providing practical
guidelines to maintain the genetic diversity and pheno-
typic resilience required for corals to survive and pro-
duce genetically diverse and viable offspring that could
serve as raw material for natural selection. Layering
both evolutionary and ecological components will maxi-
mize the resilience of restored coral populations.
The need for concrete guidelines is particularly press-
ing in the Caribbean, where investments in active
restoration of coral populations have occurred over the
last two decades and continue to increase at a rate that
exceeds similar efforts in other regions (Young et al.
2012, Chamberland et al. 2015, Lirman and Schop-
meyer 2016). Caribbean reefs also tend to be highly
degraded and suffer from long-term recruitment failure
of the two major reef-building species, Acropora palmata
(Williams et al. 2008) and Orbicella faveolata (Hughes
and Tanner 2000), Although some reefs still feature sub-
stantial stands of these species, without sexual recruit-
ment they may already be effectively extinct (Honnay
and Bossuyt 2005). Most alarmingly, since there is no
ecological redundancy in the Caribbean to replace these
species in their reef-accretion function, many Caribbean
reefs have shifted from net accretional to net erosional
states (Kuffner and Toth 2016, Yates et al. 2017). Shifts
to net erosional states are now a global phenomenon
(Perry et al. 2018), with concomitant increases in the
vulnerability of coastal communities to inundation and
shoreline erosion throughout the tropical world (Beck
et al. 2018, Storlazzi et al. 2018). Although outplanting
corals using nursery-propagated stock can help restore
some ecological functions (Montoya Maya et al. 2016)
and may buy time to prevent regional extirpation, with-
out sexual recombination and the shuffling of alleles to
promote adaptation, the long-term future of these corals
appears bleak.
The guidelines presented here aim to re-establish popu-
lations that are capable of sexual recruitment and genetic
exchange (Fig. 1). These include recommendations on
how different reef habitats should be strategically sam-
pled to capture much of the adaptive genetic variants
existing in coral populations, and how sampled genets
should be outplanted and monitored. We discuss possible
enhancements to restoration practices such as routine
genotyping of propagated stock, trait-based assessment
of genet performance, jump-starting genetic admixture by
producing first-generation offspring for outplanting, and
promoting long-range genetic exchange (“assisted gene
flow,”AGF). In addition, because corals host
Article e01978; page 2 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

photosynthetic micro-algae [family Symbiodiniaceae
sensu LaJeunesse et al. (2018)], we also consider possibili-
ties for the management of endosymbiont diversity in
restored populations. Finally, we discuss the balance of
risks and benefits associated with implementing the rec-
ommended strategies. The review is the product of the
Obtain three to six genets from diverse local environments
- Establish in nursery
- Genotype animals
Assess genet performances
Replace poorly performing
genets with new wild
collected genets
nurseries restoration sitessource colonies
Site selection
Monitor biometrics
Novel/historical habitats
Batch culture gamets
to produce genetical-
ly diverse population
of larvae
Aquire genets for propagation
Out-planting and community restoration
Propagating sexual recruits
Tag and plant four to six
genets
Add additional
genets as neces-
sary
Obtain eggs and
sperm from six
or more genets
Outplant growing
juveniles to
restoration sites
Settle larvae on substrate and cultivate
growing junveiles, minimize selection
Monitor biometrics
-partial mortality
-wound healing rate
-skeletal growth rate
-bleaching and infectious disease traits
- sexual reproductive output
N
Distant locations
( )
FIG 1. Overview of basic restoration guidelines to maximize the adaptive potential of reef-building corals facing a rapidly changing
environment. A genet is defined as a genetically unique colony or collection of colonies (ramets) that can trace their ancestry back to
the same sexual reproductive event (i.e., they stem from the same settler and, hence, share the same genome).
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 3

Coral Restoration Genetics Working group, one of the
five original working groups of the Coral Restoration
Consortium (Appendix S1: Section 1).
PRIORITIZING CORAL SPECIES FOR RESTORATION EFFORTS
Coral species selection for restoration will depend
upon the goals of the project, which could include shore-
line protection, fisheries habitat provisioning, species
conservation, tourism, or a combination thereof. Given
that funding, nursery space, and time are limited, we
propose that ecosystem-based restoration efforts for
Caribbean corals should prioritize species that are (1)
foundation reef builders; (2) experiencing severe declines
in cover (Appendix S2: Fig. S1); and (3) consistently fail-
ing to sexually recruit (Fig. 2). In the Caribbean and
western north Atlantic, only a limited number of coral
species build reef framework, the overall species diversity
is lower, and functional redundancy is limited compared
to the Indo-Pacific (Bellwood et al. 2004), making spe-
cies selection comparatively straightforward. There is a
striking lack of sexual recruitment for many of the
framework-building species throughout the basin
(Hughes and Tanner 2000, Edmunds and Elahi 2007,
Williams et al. 2008, Davies et al. 2013a) and recruit-
ment has shifted from long-lived broadcast-spawning
species to more weedy brooding species (Rogers et al.
1984, Hughes and Tanner 2000, Green et al. 2008, but
see Vermeij et al. 2011).
Current restoration efforts target Acropora cervicornis,
A. palmata,Orbicella faveolata,andO. annularis. All are
broadcast-spawning species and are among those experi-
encing widespread population declines and sexual recruit-
ment failure (van Woesik et al. 2014). A. cervicornis takes
up the most space in current nurseries (Lirman and
Schopmeyer 2016). On some reefs in Belize and the
Dominican Republic, A. cervicornis has been restored to
high densities (Lirman and Schopmeyer 2016) and out-
plants are spawning (Carne and Baums 2016). In Florida,
ashifttoA. palmata and multi-species restoration with
an emphasis on reef-building is now underway. Addi-
tional efforts have been extended locally to species where
extirpation might be imminent (i.e., Dendrogyra cylindrus
in the Florida Keys). We suggest that efforts be expanded
to target Pseudodiploria spp., Siderastrea siderea,
Stephanocoenia intersepta,Montastrea cavernosa,
Colpophyllia natans,andOrbicella franksi, as these species
each meet two prioritization criteria (Appendix S2:
Fig. S1), are already managed in some locations, and are
good candidate species for rebuilding reef structure long-
term, in part because these species still successfully pro-
duce sexual recruits.
For coral taxa that are rare or not major reef builders
(e.g., Dendrogyra,Agaricia,Porites,Dichocoenia,Favia),
we propose strategic genetic banking as a complemen-
tary activity to active restoration (Hagedorn et al. 2012).
This compromise will free up resources for major reef
builders of immediate concern while safeguarding
genetic material for future action on these rare members
that increase community diversity and may play impor-
tant, if unknown, roles in ecosystem processes (Bellwood
et al. 2006). Thus, efficient cryo-banking techniques
should be developed for species whose gametes can be
collected, and ex situ gene banking (i.e., keeping live ani-
mals in aquaria) might be considered for others. We also
recommend that restoration feasibility studies be con-
ducted for rare species experiencing massive population
declines, multi-year sexual recruitment failure, and those
that exhibit unique life histories such as Dendrogyra
cylindrus (Neely et al. 2018, Chan et al. 2019), to help
identify and address challenges associated with restoring
these species. Lastly, we propose that species prioritiza-
tions should follow an adaptive management strategy
under which demographic monitoring of natural and
outplanted populations is evaluated every 5–10 years to
determine changes in population growth rates (k)orsex-
ual recruitment rates (which serve as a reasonable proxy
when kcannot be estimated). Sexual recruitment rates
can be monitored via both recruitment tiles (Humanes
and Bastidas 2015) and genotyping (Box 1; Tables 1, 2;
Appendix S3: Section S1).
CHOOSING CORAL COLONIES FOR RESTORATION:WHO AND
FROM WHERE?
Active restoration of the major Caribbean reef
builders, specifically the acroporids and the orbicellids,
is well underway, and restoration practitioners have
already chosen many genets for propagation and out-
planting. The classical precept of primum non nocere
(“first, do no harm”) has traditionally been translated
into precautionary concerns about genetic risks, espe-
cially preventing genetic swamping or outbreeding
depression from affecting the integrity of local popula-
tions (Edmands 2007). This premise underlies why the
sourcing of restoration material from local areas has
been preferred traditionally. This “local is best”(LIB)
provenance strategy is sometimes operationally regu-
lated (Tringali et al. 2007), placing strict limits on the
geographic range of sourcing corals. However, the poor
performance of most local coral populations in recent
years suggests that whatever local adaptation is present
in these populations may not be adequate to assure per-
sistence as environments continue to change (Williams
et al. 2008, 2014b, Chan et al. 2019). Hence, we advise
considering more flexible provenancing strategies.
Plant restoration planners have similarly articulated
provenance strategies that may improve the prospects
for climate adaptation in restored populations (Sgr
o
et al. 2011, Williams et al. 2014a, Prober et al. 2015,
Espeland et al. 2017). The simple approach of selecting
warmer adapted genets assumes that predictions of envi-
ronmental conditions are known and that there are no
ecological trade-offs in phenotypes (e.g., poor reproduc-
tive performance or poor disease resistance in heat-toler-
ant genets). Hence, a so-called “climate-adjusted
Article e01978; page 4 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

provenance”strategy (sensu Prober et al. 2015) is
favored, which incorporates representation of both local
genets and genets from across an environmental gradient
skewed toward those coming from populations already
experiencing predicted future environmental conditions
(Fig. 1).
Assisted gene flow
A climate-adjusted provenance strategy is recom-
mended when designing assisted gene flow (AGF)
interventions. Such AGF interventions recognize that
local adaptation is a characteristic of local populations
that can be used to improve the fitness of distant popula-
tions, especially in scenarios of rapid environmental
change. Deliberate translocation of organisms, propag-
ules, or genes among populations can be an effective
means to facilitate the spread of adaptive alleles, particu-
larly in areas where populations have declined to the
point where colony density or genetic diversity may be
insufficient to support successful sexual production of
offspring (e.g., where only one known genet persists,
Box 1: Determining genetic and genotypic diversity of coral hosts and symbionts
Coral host genotypic diversity: In this review, we discuss the importance of both genotypic and genetic
diversity on restoration decisions. A “genet”is defined as a genetically unique colony or collection of colo-
nies (“ramets”) that can trace their ancestry back to the same sexual reproductive event (i.e., they stem from
the same settler and, hence, share the same genome). Genotypic diversity is the total number of genetically
distinct individuals (genets) within a population, whereas genetic diversity is the amount of variation
between genotypes on the level of individual genes (Fig. 3). To track the genotypic diversity of corals and
their symbionts, it is necessary to determine their unique multilocus genotypes (MLGs) via genetic analysis
(Appendix S3: Section 1). While various genotyping approaches have been developed for many of the Car-
ibbean coral species, including allozymes, amplification fragment length polymorphisms (AFLP),
microsatellites, and single nucleotide polymorphisms (SNPs; Table 1), the latter two are more routinely
used in conservation genetics today (Puckett 2017). Furthermore, microsatellite and SNP loci provide
higher allelic variation that can be used to discriminate colonies that share a MLG because they were gen-
erated via asexual fragmentation versus those colonies that share an MLG because they are closely related
(such as siblings).
Tracking symbiont community diversity is also recommended for fragments and reasonably sized juve-
niles when possible (see Role of Symbionts). The resolution of Symbiodiniaceae genotypic diversity is con-
strained by the genetic tools available. The standard internal transcribed spacer 2 (ITS2; LaJeunesse 2001)
and chloroplast 23S (cp23S; Santos et al. 2002) rDNA markers are usually sufficient to resolve symbionts
to approximately the species level. High-throughput methods for ITS2 have been developed (Arif et al.
2014, Quigley et al. 2014, Thomas et al. 2014, Smith et al. 2017), although they inevitably underestimate
diversity because ITS2 does not resolve all Symbiodiniaceae species (Parkinson et al. 2015b). Methods thus
need to be adjusted depending on whether a particular colony is expected to host only one numerically
dominant symbiont species (in which case direct sequencing is appropriate) or if it hosts multiple co-domi-
nant symbiont species (in which case denaturing gradient gel electrophoresis or high-throughput amplicon
sequencing are required; Pochon et al. 2018). Finer-scale resolution of symbiont diversity at the sub-species
level could be provided by the psbA minicircle non-coding region (Moore et al. 2003, Barbrook et al. 2006,
LaJeunesse and Thornhill 2011), microsatellites (Table 1), or SNP markers (currently under development).
Genotyping technology: With the increasing scale of restoration activities, genotyping efforts need to be
simplified at minimal costs (Appendix S3: Section 1). Technological advancements in high-throughput
SNP-based methods such as genotype-by-sequencing (GBS) and reduced representation sequencing meth-
ods (collectively called RAD-seq) have made it possible to assess genetic diversity at a large number of sin-
gle nucleotide variant (SNV) loci for a reasonable cost (Altshuler et al. 2000). However, there is no
guarantee that the same set of SNV loci is recovered from each sample in a run or between runs, making
clone identification more challenging. Other SNP-based methods using standardized markers, such as tar-
get-enrichment capture, RAD capture (Hoffberg et al. 2016), microarrays, and microfluidics, also provide
information on the order of 10
2
–10
5
of variants reproducibly (Table 2; Dixon et al. 2016). Regardless of
which new approach is chosen, all these methods present additional hidden challenges, requiring advanced
bioinformatic training, computational infrastructure, and increased data storage (Table 2). Because
resource allocation is an important consideration for practitioners when selecting a genotyping method, we
consider two options in depth for obtaining coral MLGs based on the availability of common laboratory
equipment, computational resources, and overall budget (Appendix S3: Section S1).
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 5

(Baums et al. 2006, 2014b). Foundation species with
wide ranges and large population sizes can be
particularly good candidates for AGF to yield ecosys-
tem-scale benefits (Aitken and Whitlock 2013). Many
coral species fit this profile, and AGF was suggested as a
viable management strategy for corals as long as a
decade ago (Hoegh-Guldberg et al. 2008, Riegl et al.
2011).
Embracing AGF interventions has been suggested by
several studies (Hoegh-Guldberg et al. 2008, Dixon
et al. 2015, Matz et al. 2018) because corals adapt to
local temperature conditions at the genetic level (Polato
et al. 2010, Bay and Palumbi 2014, Palumbi et al. 2014,
Dixon et al. 2015) and therefore genetic variants con-
ferring heat tolerance should already be present at high
frequencies in warm-adapted populations. In some
cases, natural migration appears to be sufficient to
exchange these adaptive genetic variants among ther-
mal environments (Matz et al. 2018). Nevertheless,
assisted translocation could help ensure such exchange,
especially because warming ocean temperatures are
expected to change dispersal patterns by shortening
planktonic periods and altering current speeds and
direction (Heyward and Negri 2010, Baums et al. 2013,
Figueiredo et al. 2014, Wood et al. 2016). Models
based on population genetic data from Acropora mille-
pora, a common coral on the Great Barrier Reef, show
that even when immigrants account for as much as 1–
3% of the total population there is still no risk of “mi-
grational meltdown”(a reduction of fitness of local
population because of an influx of maladaptive alleles)
(Matz et al. 2018). This suggests that human-assisted
migration would not pose risks for coral populations
still numbering in the tens of thousands, although this
may become an issue for populations that have experi-
enced severe declines, such as those in the Florida Keys.
Another consideration is the possible limiting effects of
cold tolerance when out planting corals sourced from
warner environments to colder ones (Howells et al.
2013).
Nursery and breeding stock selection
In situ nurseries have become an important source for
coral stock used in outplanting and breeding efforts.
One goal of a nursery should be to ensure good repre-
sentation of adaptive alleles that are beneficial in various
present-day reef environments, encompassing a sizeable
portion of adaptive genetic diversity existing within the
species. At this time, we rely on only a handful of traits
to identify resilient coral colonies that may carry poten-
tially adaptive alleles, we do not know the identity of the
potentially adaptive alleles, and we have very few reliable
biomarkers (Box 2). Therefore, we propose the following
strategies to maximize the chance that nursery collec-
tions will capture alleles that help coral species adapt to
various environments (Fig. 3).
Box 2: Biomarkers
Biomarkers have emerged as useful tools in many
fields, from plant breeding to human disease predic-
tion. Recently, they have been suggested as attractive
candidates for use in coral restoration. In theory,
restoration practitioners would use a simple bioassay
to uncover information about coral colony perfor-
mance. This information could then be applied to
select colonies for parental stocks in larval propaga-
tion, rearing in nurseries, or matching outplants to
particular sites in anticipation of future environmen-
tal challenges. However, biomarkers are often con-
text- and species-specific (Parkinson et al. 2018a),
and therefore multiple markers may be needed
depending on the types of information desired. In
addition, there are many steps between identifying a
potential biomarker and deploying it in the field, and
the intermediate steps involved in biomarker devel-
opment are often overlooked. The process involves
four major phases: discovery, validation, field trials,
and implementation. At present, the majority of
basic scientific research has not progressed past the
discovery phase (Parkinson et al. 2018a). Conse-
quently, the costs associated with developing practi-
cal biomarkers as predictive tools for selective
restoration may be high. While the potential savings
in terms of time and effort may justify the initial
investment, a cost-benefit analysis must be consid-
ered when prioritizing funding for further research in
this area at this time.
1. Identify environmentally diverse source reef patches.
Within the largest practical area, identify reef sites
that differ in their environmental conditions. Ideally,
as part of a climate-adjusted provenance strategy,
some of these sites would feature projected future
conditions, such as elevated temperature, more vari-
able temperature regimes, and/or lower aragonite sat-
uration state. Our current understanding is that local
adaptation in corals happens most prominently with
respect to depth (Bongaerts et al. 2011, Prada and
Hellberg 2013, Cohen and Dubinsky 2015). But other
factors can play a role in adaptation such as tempera-
ture (Howells et al. 2013), especially its daily range
(Palumbi et al. 2014, Kenkel et al. 2015a). Other
environmental parameters such as pH (Comeau et al.
2014, Schoepf et al. 2017), turbidity (Anthony 2000,
Anthony and Fabricius 2000), or levels of inorganic
nutrients may also play a role in local adaptation,
though more research into these specific factors will
be required. Even in the absence of detailed environ-
mental data, distinct reef habitats can be identified as
Article e01978; page 6 ILIANA B. BAUMS ET AL. Ecological Applications
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sites hosting noticeably different communities of reef
organisms. For the success of the sourcing strategy it
is important to sample as widely as possible along
environmental gradients, in the same depth range as
the target restoration sites. The latter is because cor-
als from deep reef habitats (>15–20 m) may be
TABLE 2. Comparison of the microsatellites and SNP genotyping methods
Measure Msats
SNP-based methods
Targeted-enrichment
capture Microarray Microfluidics
Traditional
GBS/RAD-tag RAD capture
No. markers 10
1
10
2
10
3
–10
5
10
2
10
3
–10
5
10
2
–10
3
Minimum no. samples 1 6 96 96 1 1
Sample preparation†moderate moderate low-moderate low low-moderate low- moderate
Technical expertise‡moderate high moderate moderate-high high moderate
Computational resources§low high moderate moderate high moderate
Reproducible between labs¶moderate high high high high high
Estimated price per sample US$50 US$450 US$50 US$10 US$75 US$50–70
†Low, library preparation and sequencing can be completed at a core-facility provider; moderate, multiple-day process but
limited hands-on time.
‡Based on training requirements. Low, minimal training; moderate, some advanced training; high, highly advanced training
(Grover and Sharma 2016).
§Based on the computational resource demands. Low, analyzed on a standard computer with minimal storage; moderate, analyzed
on standard computer with large data storage requirements; high, analyzed on high-performance computer with large data storage.
¶Sensitivity of the method to differences between laboratories or sequencing facilities. Moderate, analysis can be impacted by
laboratory conditions (e.g., different PCR buffer or PCR machine can result in loci running at different sizes) and experience of
user; High, analysis can be impacted by high sequencing error rates, but genotype calls are not influenced by user.
TABLE 1. An overview of different genotyping methods employed for Caribbean coral species and their symbionts.
Species Allozymes AFLP Msats SNPs References
Coral
Acropora cervicornis U(12) UBaums et al. (2005a, 2009), Drury et al. (2016)
Acropora palmata UU(13) UBaums et al. (2005a, 2009), Devlin-Durante and
Baums (2017)
Dendrogyra cylindrus U(11) Chan et al. (2019)
Favia fragum U(15) Carlon and LippE (2008)
Orbicella annularis UUU(14) UVan Veghel and Bak (1993), Lopez et al. (1999),
Fukami et al. (2004), Severance et al. (2004),
Davies et al. (2013b), Prada et al. (2016)
Orbicella faveolata UU(9) UFukami et al. (2004), Lopez et al. (1999),
Davies et al. (2013b), Prada et al. (2016)
Montastrea cavernosa UU(14) Shearer and Coffroth (2004), Brazeau et al. (2013),
Serrano et al. (2014), Jarett et al. (2017)
Porites astreoides UUU(15) Weil (1992), Brazeau et al. (1998), Shearer and
Coffroth (2004), Kenkel et al. (2013), Serrano et al. (2016)
Symbiont
Symbiodinium
microadriaticum
(ITS2 type A1)
USchoenberg and Trench (1980)
S. “fitti”(ITS2 type A3) U(13) Baillie et al. (2000a,b), Pinz
on et al. (2011),
Baums et al. (2014a)
Breviolum “dendrogyrum”
(ITS2 type B1)
U(7) Santos and Coffroth (2003), Pettay and LaJeunesse (2007),
Chan et al. (2019)
B. endomadracis
(ITS2 type B7)
U(3) Santos and Coffroth (2003), Pettay and LaJeunesse (2007)
B. minutum (ITS2 type B1) U(3) Santos and Coffroth (2003), Pettay and LaJeunesse (2007)
B. psygmophilum
(ITS2 type B2)
U(6) Pettay and LaJeunesse (2007), Grupstra et al. (2017)
Durusdinium trenchii
(ITS2 type D1a)
U(17) Pettay and LaJeunesse (2009), Wham et al. (2011)
Notes: AFLP, amplification fragment length polymorphism; Msats, microsatellites; SNPs, single nucleotide polymorphisms. A U
indicates that the method was used for that species. Numbers in parenthesis give the number of microsatellite loci available.
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 7

partially or completely reproductively isolated from
shallow populations of the same species (Prada and
Hellberg 2013, Serrano et al. 2014, 2016, Bongaerts
et al. 2017) and may be unsuitable for propagation in
shallow nurseries or for restoration of shallow sites.
2. Select colonies for propagation. Collect three to six
coral genets per patch, selecting healthy colonies that
show some difference in morphology and/or size.
They should be growing some distance apart (>5 m;
Baums et al. 2006, Foster et al. 2007) to maximize
the chance of sampling distinct genets rather than
clonemates (Box 1). Collecting just a few colonies per
patch might seem insufficient but just three or four
diploid colonies would contain about one-half of all
common alleles (frequency >5%) present in a popula-
tion (Fig. 3). Thus, sampling of three to four colonies
from a patch would capture many, if not most, alleles
that are locally adaptive since such alleles are
expected to be common within the patch due to natu-
ral selection.
3. Monitor, replace, and repeat. Propagate selected
colonies in the nursery and monitor their perfor-
mance (see Phenotypic traits of propagated corals). If
some corals show poor fitness in the nursery, replace
them with other genets from the same patch or habi-
tat type. Excluding poorly performing genets is unli-
kely to affect representation of the adaptive genetic
diversity in the nursery provided representation of all
habitat types is maintained. However, it is possible
that local adaptation to some reef environments
would prove incompatible with the nursery, which is
itself a distinct habitat. Although genetic variants in
these corals are still valuable as part of the adaptive
genetic diversity of the species, we suggest triaging
Genet 1 Genet 2
Genet 3 Genet 4
Genet 5
Parent colonies release egg/sperm
bundles
F
new genets
owth from
single larva
Asexual repr agmenta-
Genet 5
Ramet 1 Ramet 2
Planula larvae
Primary polyps
A
B
FIG 2. Coral reproduction. (A) Most reef-building species in the Caribbean are self-incompatible hermaphroditic broadcast spawn-
ers. Adult colonies release egg–sperm bundles that float to the surface where they break apart and mix with gametes from other colonies
of the same species. After fertilization and development, larvae settle onto the reef, metamorphose into primary polyps, and grow into
new genets. (B) Over time, genets may fragment. These fragments can reattach to form new ramets of the same genet. A genet is defined
as a genetically unique colony or collection of colonies (ramets) that can trace their ancestry back to the same sexual reproductive event
(i.e., they stem from the same settler and, hence, share the same genome). Adopted from Devlin-Durante et al. (2016).
Article e01978; page 8 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

such cases (i.e., omitting genets that perform poorly
in nurseries) or omitting the nursery stage by rearing
fragments at the native reef (protocols for this are
under development; Fragments of Hope, personal
communication). If survival and growth is merely sub-
optimal in nurseries rather than absent, then propa-
gating poorly performing genets in the nursery at a
minimal level may be warranted if they are perform-
ing particularly well during outplanting and have
other desirable traits (O’Donnell et al. 2018).
The resulting minimum number of coral genets for
each species propagated in a nursery should be on the
order of 20–25 and include representatives from reef sites
spanning the full range of environmental variation occu-
pied by the species within the restoration jurisdiction.
This number of genets would contain >95% of the com-
mon alleles present locally within a species (Fig. 3). This
approach still omits most of the genetic diversity existing
within a species simply because the clear majority of nat-
ural genetic variants are rare. In fact, by far the most
common type of genetic variant is a singleton, an allele
present in a single genet of the species. However, to cap-
ture these would require sampling essentially all genets
in a species, an approach that is not practical. Rare alle-
les are by no means useless; while they might not be
adaptive at present (given their low abundance) they
might become adaptive in the future, when conditions
change. Indeed, long-term adaptation will eventually
require replacement of present-day common adaptive
alleles with new ones that are currently rare or even non-
existent (requiring a new mutation to arise). Despite this,
comprehensive sampling of alleles that are currently
common serves a very important purpose: it gives the
restored population a better chance of surviving in the
immediate future. With climate-adjusted provenancing,
survival trajectories might be extended by several dec-
ades. The longer-term survival of a restored population
will only be ensured if gene flow occurs with adjacent
populations (introducing immigrants from other popula-
tions that bear novel adaptive alleles), or if adaptive
mutations occur within the restored population.
Sexual propagation and selection of donor colonies
The short-term adaptive response based on common
alleles outlined in the previous section can only happen
if outplanted genets reproduce sexually to generate novel
allele combinations. Without offspring of such crosses
recruiting back to the restored reef, the scope for natural
selection cannot extend beyond the originally outplanted
genets, and no further adaptation would be possible
(barring somatic mutations and genotypic mosaicism;
Van Oppen et al. 2011). In this regard, outplanting hun-
dreds or thousands of lab-reared, sexually produced off-
spring instead of (or in addition to) adult coral
fragments is promising because it would accelerate the
process of genetic restoration by one generation. Out-
planting sexually produced offspring would be especially
valuable for species experiencing long-term failure of
natural recruitment, such as the Caribbean acroporids
and orbicellids. Currently in the western Atlantic, game-
tes for larval production are harvested from wild popu-
lations, as well as from fragments in nurseries, via colony
netting and subsequent ex situ fertilization in culture
vessels. Larval offspring are eventually returned to the
field at various stages of development. Sexual propaga-
tion and selection of donor colonies should be based on
the following strategies.
Maximize fertilization success.—Most major reef-build-
ing coral species are broadcast spawners that are highly
0
0.2
0.4
0.6
0.8
1.0
0 5 10 15 20
Proportion of common alleles
represented
Genets sampled
DCBA
FIG 3. Capturing allelic diversity for coral conservation. Sampling of relatively few genets from a population is sufficient to cap-
ture most common alleles. (A) Proportion of alleles observed when sampling a certain number of genets (N
ind
) from a population,
depending on the allele frequency. For an allele of frequency P, the probability of not observing it among Ndiploid genets is
(1 P)
2N
. Hence, the probability of observing such an allele, which is the same as the proportion of such alleles across the whole genome
that are observed, is 1 (1 P)
2N
. (B) The proportion of common alleles (allele frequency P>0.05) depends on their allele frequency
in three species of reef-building corals and can be calculated based on single nucleotide polymorphism (SNP) data. The three species
(Acropora millepora,Orbicella faveolata,andAcropora cervicornus) have broadly similar distributions of their common alleles, despite
substantial phylogenetic and geographic separation. (C) Proportion of common SNP alleles represented within a certain number of sam-
pled genets. A sample of just three genets captures >50% of all SNP alleles found in more than 5% of all genomes in the population, and
12 genets capture 90% of them. (D) Proportion of common alleles represented calculated based on microsatellite loci for Acropora
palmata. Note that due to higher mutation rate of microsatellites they require four rather than three genets to represent >50% of alleles.
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 9

outbred and genetically diverse (Baums 2008, Baird
et al. 2009). Therefore, it is usually not necessary to
determine their relatedness to avoid inbreeding because
the likelihood of picking two parents in natural popula-
tions that are closely related as a result of sexual repro-
duction (i.e., are siblings) is vanishingly low (Fig. 2). It
must be noted, however, that some Caribbean reef
builders (Acropora spp., Orbicella spp., D. cylindrus) can
be highly clonal (Fig. 2), where neighboring colonies are
genetically identical due to asexual fragmentation
(Baums et al. 2006, Foster et al. 2007, Miller et al.
2017). These species are hermaphroditic, but are practi-
cally self-incompatible, and consequently successful sex-
ual reproduction requires gametes to be available from
(at least) two different genets (Fogarty et al. 2012,
Baums et al. 2013). To minimize the chance of harvest-
ing gametes from the same genet, it can be helpful to
sample colonies that are relatively far apart (>5m)
(Baums et al. 2006, Foster et al. 2013). The only defini-
tive solution to the clonality problem is to genotype
sampled corals (Box 1), which is highly recommended if
the budget allows (Appendix S1–S3). Because broad-
cast-spawning species typically acquire their algal sym-
bionts from the environment horizontally each
generation, effects of breeding design on the population
structure and diversity of these symbionts are not a
major concern (however, the situation may be different
for species that transmit their Symbiodiniaceae from
parent to offspring vertically each generation; see Role
of Symbionts). In some regions, sexual compatibility can
be surprisingly low among conspecific Caribbean acrop-
orids and orbicellids (Fogarty et al. 2012, Baums et al.
2013, Miller et al. 2017), for unknown reasons. For
example, there are no data supporting the notion that
corals from contrasting environments have lower cross-
fertilization rates. Dixon et al. (2015) crossed colonies
from very different thermal regimes and did not observe
any differences in fertilization rates (it was nearly 100%
for both between- and within-population crosses). In
addition, the typical lack of genetic structure across envi-
ronmental gradients for broadcast-spawning corals
speaks of the absence of strong reproductive barriers
imposed by environmental differences (Ayre and Hughes
2000, Baums et al. 2005b, Davies et al. 2015b), except
across large depth gradients (Prada and Hellberg 2013).
Whether sexual compatibility is determined entirely by
genetics or is also context-dependent remains an open
question. Nevertheless, because even a modest percent-
age of unfertilized eggs in larval cultures can cause sig-
nificant overall mortality (Pollock et al. 2017), the
fertilization success of a coral genet should be monitored
whenever possible to improve breeding outcomes. Fertil-
ization success between two-parent crosses is easily mea-
sured by counting the proportion of cleaving eggs two
hours post-fertilization, whereas measuring fertilization
success of single parental genets in batch cultures
requires genotyping of offspring (Baums et al. 2013,
Davies et al. 2015a). Fertilization success is highly
dependent on gamete concentration (Oliver and Bab-
cock 1992, Levitan et al. 2004) with optimum in the
range of 10
6
cells/mL. Because, fertilization also declines
with gamete age (Oliver and Babcock 1992, Fogarty
et al. 2012), the recommended strategy is to use fresh
gametes whenever possible. Maximizing parental diver-
sity of batch cultures (more than two parental donors) is
the next most important goal. Detailed instructions on
how to increase larval survival rates are available from
The Nature Conservancy (2018).
Use larval crosses to increase local genetic diversity or
sexual recruit numbers.—During spawning, gamete out-
put is often disproportionate, where one genet provides
more spawn than other parents. When designing batch
cultures, considerations about the combination of par-
ents and the relative contribution of each parent to the
batch will depend on the goal of the breeding program.
If the goal is to maximize the genetic diversity of off-
spring, it is important to ensure equal contribution of
parents to the batch culture. However, if the goal is to
create the largest number of larvae regardless of their
genetic diversity, then all gametes should be added to
the culture. We propose that batch cultures for restora-
tion should include at least six parents (Iwao et al.
2014), and more when possible.
Maximize settler survival.—Survival of outplanted
recruits is currently low and presents a bottleneck to the
success of sexual recruitment strategies. However, exam-
ples of sexual recruits that have survived to sexual matu-
rity and now spawn predictably each year exist (Guest
et al. 2014, Chamberland et al. 2016, dela Cruz and
Harrison 2017). Settlers survive better when competition
with benthic macro- and turf algae is low and predation
pressure from coral predators is reduced (e.g., Her-
modice carunculata,Coralliophila abbreviata), thus care-
ful site selection for outplanting is paramount (see
Outplanting strategies).
Enhance adaptation potential via assisted gene flow.—
Crossing corals and outplanting offspring may be a par-
ticularly effective means of AGF. Donor colonies
sourced from widely separated and environmentally
divergent reefs might be expected to show low survivor-
ship if directly transplanted from one site to another. In
contrast, their first-generation offspring would be
expected to show greater phenotypic variation, allowing
at least some of them to thrive in either parental habitat.
In corals, non-heritable maternal effects can also have an
important impact on the physiology and stress tolerance
of early life cycle stages (Dixon et al. 2015, Kenkel et al.
2015b). This can potentially be harnessed to further
improve the chance of survival of first-generation off-
spring upon transplantation: whenever possible, mothers
(i.e., egg donor colonies) should come from the habitat
into which the first-generation offspring are going to be
outplanted. While the occurrence of outbreeding
Article e01978; page 10 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

depression has never been directly tested in corals, obser-
vations in other animals as well as plant species indicate
that the risk of outbreeding depression is likely low and
should not prevent coral restoration action, especially in
local populations that are rapidly declining (Ralls et al.
2018).
Interspecies hybridization.—Scleractinian corals have a
long history of interspecies hybridization (Veron 1995).
General evolutionary principles dictate that the long--
term fitness of hybrids must be lower than the fitness of
the “purebred”species, otherwise the species would have
merged and would not exist as separate units. However,
if hybrids can successfully back-cross (reproduce with
the purebreds), they could provide a way to exchange
adaptive genetic variation among constituent species.
Hybrid corals occur naturally in the Indo-Pacific as well
as the Caribbean (Willis et al. 2006). In Caribbean acro-
porids, hybrids between A. palmata and A. cervicornis
exhibit a wide range of morphological variation, and
are often found in very shallow, high light environments
(Vollmer and Palumbi 2002, Fogarty 2012). As a source
for novel morphological diversity, hybridization is an
attractive restoration target to enhance reef habitat
structure (though clearly not for species recovery).
There is little concern about genetic swamping of paren-
tal species with hybrid alleles: although these hybrids
produce viable gametes (Fogarty 2012), later generation
genets are still rare in the population and both parental
species have very low rates of successful natural sexual
reproduction. In the Orbicella species complex, inter-
species hybrids are also observed but occur at different
frequencies across the Caribbean and perhaps over
depth gradients (Fukami et al. 2004). In both hybrid
complexes, the hybrid phenotypes may be useful for
unique restoration applications such as restoring reef
structure in deep, very shallow, or sheltered habitats.
Additionally, preliminary lab studies have verified that
hybrid Acropora offspring can show improved perfor-
mance in exposure to elevated temperature and CO
2
conditions. The limited space in nurseries may dictate
that practitioners prioritize rearing purebred parents,
but at least for sexual larval production, gametes of
opportunity may be used to generate interspecies
crosses. The outplanting strategy for these hybrid set-
tlers should follow the same recommendations as for
the purebred parents (see Outplanting Strategies).
Phenotypic traits of propagated corals
Given the lack of predictive tools for selecting genets a
priori (Box 2), genets will likely perform differently dur-
ing the propagation phase than they do on the native
reef. Performance depends on interactions between gen-
ets and their local environment that are difficult to pre-
dict (Lirman et al. 2014b, Drury et al. 2017, O’Donnell
et al. 2018) and trade-offs between desirable traits, such
as growth and thermal tolerance, may occur (Ladd et al.
2017). Thus, maintaining phenotypic diversity in out-
plant populations is essential. To that end, tracking key
traits in nursery populations will not only help restora-
tion practitioners optimize nursery stocks but can ensure
that a diverse suite of potentially important traits is
included in outplanting designs. However, traits are not
all equally relevant to success and measuring some traits
can be challenging, time consuming, and cost pro-
hibitive, diverting resources from essential tasks such as
outplanting and nursery maintenance. Therefore, estab-
lishing consistent practical guidelines for collecting the
most informative data will be important to optimally
manage nurseries.
While most genets can survive and propagate in nurs-
ery conditions, there are often more genets available
within a nursery’s area of interest than can be main-
tained. When this is the case, traits that can help guide
which genets to propagate are (1) partial mortality, (2)
rate of wound healing, (3) skeletal growth rate, (4)
bleaching and infectious disease resistance or resilience,
and (5) sexual reproductive output (Table 3).
Partial mortality.—Partial mortality is common in coral
colonies due to a variety of impacts, including coral-
livory, competition, fragmentation, and temperature
stress (Lirman et al. 2014a). Partial mortality can lead
to increased susceptibility to infectious diseases. Thus,
percent recent mortality is a reliable indicator of recent
stress across a range of coral species (Cooper et al. 2009,
Lirman et al. 2014a) and can be visually estimated
directly or from photographs.
Wound healing rate.—Corals that heal rapidly after sus-
taining lesions or fragmentation have a lower probability
of secondary infection (Palmer et al. 2011) and therefore
higher probability of survival. Furthermore, healing rate
may be indicative of improved physiological condition
(Fisher et al. 2007) and/or greater energy reserves (Denis
et al. 2011), which can help corals survive bleaching
events (Rodrigues and Grottoli 2007, Levas et al. 2013,
2018, Grottoli et al. 2014, Camp et al. 2018).
Skeletal growth rate.—Corals that grow rapidly in nurs-
eries (i.e., high calcification rate) can be fragmented more
frequently to produce more stock. Corals that grow
rapidly in the field generate more structural complexity,
which is often a primary goal of reef restoration. Unfortu-
nately, linear extension rate (a frequently applied measure
of coral growth) is not always correlated in the nursery
and the field (O’Donnell et al. 2018) and growth rates are
often not correlated with survival (Ladd et al. 2017).
However, there is evidence that calcification rate may be
genetically influenced and therefore represents a good
measure of genet performance, whereas linear extension
rate and skeletal density vary with environmental condi-
tions (Kuffner et al. 2017). Although quantifying calcifi-
cation rate by measuring buoyant weight is time-
consuming (Jokiel et al. 1978, Herler and Dirnw€
ober
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 11

2011, Morrison et al. 2013), investing the time and
resources initially to quantify calcification in this way
when selecting genets could have long-term payoffs in
nursery and outplanting efficacy. However, for tracking
genet growth in the field, we suggest a metric commonly
used in silviculture termed the “crown area”(CA) of a
tree (Uzoh and Ritchie 1996). Crown area defines the
two-dimensional footprint under the tree canopy and,
thus, would work for branching and massive coral mor-
phologies alike, and represents the coral’scapacityfor
harvesting direct, downwelling solar irradiance. The mea-
surements needed to calculate crown area are the long
width of the crown (CWL) and the short width of the
crown (CWS, perpendicular to the long width), both of
which can be easily estimated using a tailor’s tape, and
the area of the footprint calculated using the formula
CA ¼CWL CWS p=4:
In addition to yielding important information on how
much reef-substratum area each coral colony claims per
unit of time, it is a simple and straightforward measure-
ment of planar coral-surface area with which to normal-
ize calcification rates (Kuffner et al. 2013) or other
physiological measurements.
Bleaching and disease resistance and/or resilience.—
Threats to coral reefs are numerous but disease and
bleaching are two of the main drivers of coral decline in
the wild (Halpern et al. 2008, Harborne et al. 2017) and
in restoration projects (Drury et al. 2017, Ladd et al.
2017). Importantly, infectious disease prevalence and the
frequency and severity of bleaching events are expected
to increase over the coming century (Miller et al. 2014,
Maynard et al. 2015, van Hooidonk et al. 2016) and
bleached corals are often less resistant to infectious dis-
eases (Muller et al. 2018). Therefore, to maximize the
chances of successful restoration outcomes, nurseries
should expend efforts to identify and maintain genets that
are resistant or resilient to thermal stress and disease (i.e.,
do not bleach and do not contract infectious disease, or
rapidly recover from both). Although multiple traits can
impart resilience to one or both of these stressors, such as
the identity and diversity of algal symbionts, hetero-
trophic capacity, energy reserves, and environmental his-
tory (Baker et al. 2004, Berkelmans and van Oppen 2006,
Anthony et al. 2009, Hughes and Grottoli 2013), many
of these traits are currently time-consuming or difficult to
measure, and require specialized training and equipment.
Instead, restoration practitioners should focus on simple,
qualitative surveys to track the prevalence of mortality,
bleaching, and infectious diseases among genets. Survey
data should be collected at least twice a year to coincide
with the timing of bleaching and/or infectious disease
outbreaks in that region (although more frequent surveys
are desirable). Surveys should involve recording the num-
ber and proportion of ramets from each genet experienc-
ing bleaching or disease and whether the recorded
stressor resulted in partial or complete ramet mortality,
or if the ramet survived (Muller et al. 2018). Genets that
show high mortality due to infectious disease or bleach-
ing should be replaced within the nursery, preferably from
the same source site and from parent colonies that appear
to also have recovered from the stress or were less suscep-
tible to the stress.
Sexual reproduction.—Fecundity is a necessary, but
insufficient, trait to assure reproductive success given the
requirements for spawning synchrony and fertilization
compatibility (see Sexual propagation and selection of
donor colonies). The cultivation of large adult fragments
as “spawning stocks”within nurseries can provide oppor-
tunities to monitor the presence/absence of spawning and
synchrony in spawn time among genets as well as to col-
lect and rear sexual offspring. Reproductive size will vary
considerably among species (Soong and Lang 1992) so
maintaining multiple colonies of all genets above spawn-
ing size in nurseries may be more feasible for some species
than others. Genets with low reproductive output that are
low performing in the other phenotypic trait categories
should be reevaluated as candidates for propagation
stocks. A low-cost method to assess gamete quality is to
observe sperm motility (Hagedorn et al. 2006), which is
highly predictive of fertilization success. Sperm motility
can be scored by observing live sperm through a low-end
phase contrast microscope and estimating the proportion
of sperm that are moving (M. Hagedorn, personal com-
munication). This is cheaper and faster than assessing egg
quality (e.g., by analyzing their lipid content). Sperm
motility is likely influenced by genetic factors as well as
environmental factors (such as heat stress (Hagedorn
et al. 2016)) and is consequently a good measure of genet
performance in a given environment.
OUTPLANTING STRATEGIES
The selection of sites to establish restored populations
is a strong factor in the ultimate success of outplants.
Many previous outplanting efforts show high variation
in survivorship among sites that are not easily attributa-
ble to specific ecological drivers (Bowden-Kerby 2008,
Bowden-Kerby and Carne 2012, Lirman et al. 2014b,
Drury et al. 2017). Potential contributing factors include
protection status, visitation, intact trophic structure of
TABLE 3. Phenotypic traits that can help in selecting coral
genets for propagation and restoration.
Trait Measurement
Partial mortality amount of tissue loss
Wound healing rate days to heal from fragmentation
Skeletal growth rate buoyant weight or “crown area”
Bleaching and infectious
disease resistance/resilience
no bleaching/infectious disease
or recovers quickly
Sexual reproduction output spawning and sperm motility
Article e01978; page 12 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

the reef (including herbivory and corallivory levels),
water quality, historical occurrence of the species, and
alleviation of the stressors that caused the original coral
decline (The Nature Conservancy checklist; available
online).
11
Individual species need to be outplanted to
sites within their general habitat niche (e.g., A. palmata
prefers relatively shallow, high energy habitats) but more
specific guidelines can be difficult to establish due to the
lack of baseline data, species-specific differences in
niches (Goreau 1959, Dollar 1982), and uncertainty as
to how those niches may change in the future. Historical
and fossil records may be used as guides to where species
flourished recently and during the warmer mid-Holo-
cene, providing insight for restoration siting (Toth et al.
2018).
Site selection for fragments.—Within species, there is an
expectation that genets should survive better in a habitat
similar to their native habitat. Direct reciprocal trans-
plant experiments with various species support this
expectation (Howells et al. 2013, Kenkel et al. 2013).
However, studies examining habitat-specific perfor-
mance of nursery-reared Acropora spp. do not show pat-
terns of preferential performance (e.g., in linear growth
or mortality) in native sites or habitat types (Drury et al.
2017, O’Donnell et al. 2018, Pausch et al. 2018). There
are various reasons this expectation may not play out,
such as a lack of local adaptation in the first place, or
acclimation during the nursery propagation period that
decouple this affinity. Stochastic disturbance as well as
rapid change in environmental conditions within indi-
vidual sites may also exacerbate the mismatch of genets
with native habitats. In the absence of better predictive
capacity in matching genet performance (see Box 2), our
overall recommendation is to adopt a similar climate-
adjusted provenance strategy in outplanting genets
among individual sites (Fig. 1), with proportional repre-
sentation of all genets from available stocks outplanted
among sites.
Increasing potential for sexual reproduction.—To maxi-
mize the potential for sexual reproduction in the
restored population of broadcast-spawning species,
more than one genet is required. Two genets may provide
only marginal fertilization potential for outcrossing her-
maphrodites, while mixtures of four to six parents
showed high fertilization success in Acropora spp.
(Baums et al. 2013, Iwao et al. 2014, Miller et al. 2017).
Higher numbers of parental genets (~10) are likely
needed for gonochoristic species because sex ratios are
often skewed, or for Acropora spp. due to lack of syn-
chrony during spawning and variability in fertility
among genets (Fogarty et al. 2012, Miller et al. 2016).
Hence, we recommend mixtures of 5–10 genets for batch
culturing of all species. Optimal distance between
outplants is unknown but 2–3 m may work well for fast
growing acroporids and orbicellids (not too far for suc-
cessful fertilization, not too close that colonies compete
for resources). If more genets are available in nursery
stocks, they can be allocated among sites in different
combinations or, if phenotypic information on stress-
resistant genets is available, they may be stratified
among sites to ensure that some resistant phenotypes
are outplanted to each site. In special cases where certain
genets display multiple positive traits (e.g., low partial
mortality and high skeletal growth rate), these “winners”
may be included at as many sites as feasible, keeping in
mind that these nursery “winners”may not necessarily
exhibit superior performance in the wild.
Site selection for sexual recruits.—In the case of restora-
tion based on sexual reproduction, each juvenile repre-
sents a unique genet. Thus, the number of genets
outplanted to a site will be dramatically higher than can
be achieved when outplanting nursery-reared coral frag-
ments. We propose that similar strategies in site selection
be employed for the outplanting of sexual recruits as for
fragments. The goal is to mix and match as many genets
as possible to maximize genetic diversity, which is the
basis of adaptive resilience (Hermisson and Pennings
2005, Baums 2008, Whiteley et al. 2015).
Monitoring.—It is too time consuming and challenging
to monitor very small sexual propagules, but as recruit
sizes increases, they are relatively easy to track. Subse-
quent monitoring of the success of genets within each
outplant site can provide important insights into their
performance. Where tracking the phenotypic perfor-
mance of genets across sites is feasible, resulting data
should be contributed to genet/phenotype databases (see
Future research needs). In the simpler case where the fate
of genets is not tracked, colonies that expire should be
replaced with fragments from genets that were not origi-
nally included at that site.
ROLE OF SYMBIONTS
Role of symbiont in an asexual restoration program
Reef corals are mutualistic symbioses between diverse
and taxonomically divergent taxa that collectively com-
prise the coral “holobiont”(Rohwer et al. 2001), and the
identity of these partners can have important effects on
the phenotypic characteristics of coral colonies (Baker
2003). In particular, diversity in the algal symbiont com-
munity (family Symbiodiniaceae) has been linked to
variation in holobiont thermotolerance (Glynn et al.
2001, Baker et al. 2004, Berkelmans and van Oppen
2006, LaJeunesse et al. 2010), growth rate (Jones et al.
2008, Cunning et al. 2015, Pettay et al. 2015), irradiance
optima (Rowan and Knowlton 1995, Rowan et al. 1997,
Iglesias-Prieto et al. 2004), and possibly disease resis-
tance (Correa et al. 2009), all of which are relevant to
11
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site-selection
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 13

restoration objectives. Thus, algal symbionts may affect
restoration outcomes, though evidence for such impacts
in nurseries or outplant sites is currently lacking in the
few cases where they were investigated (Lirman et al.
2014b, Parkinson and Baums 2014, O’Donnell et al.
2018, Parkinson et al. 2018b).
Because many coral species commonly used for
restoration are capable of hosting several species and
strains of Symbiodiniaceae, at least when sampled across
their biogeographic range, algal symbiont diversity may
create phenotypic and genetic differences among
restoration units that are not attributable to the coral
host (Parkinson and Baums 2014). However, unlike host
genetic differences, symbiont genetic differences may not
be fixed over a coral genet’s lifespan, as the symbiont
community can potentially change over time in response
to disturbances and/or prevailing environmental condi-
tions. However, barring direct collaboration with scien-
tists to identify and monitor changes in symbiont
communities using genetic methods, it may not be prac-
tical for most restoration practitioners to take explicit
account of Symbiodiniaceae diversity for the time being.
Although an active area of research, prescriptive meth-
ods of manipulating symbionts as part of routine nurs-
ery propagation and outplanting have yet to be
identified, and the longevity of these manipulations has
yet to be established in the field (Peixoto et al. 2017). At
present, it should be sufficient for practitioners to realize
that exposure of nursery-grown corals to specific envi-
ronmental conditions might lead to changes in symbiont
communities, leading to variation in outplanting success.
Climate-adjusted provenancing might represent a prag-
matic approach to dealing with this uncertainty. Warmer
local environments are expected to have a higher abun-
dance of both thermotolerant coral host genets and ther-
motolerant symbionts, so sourcing holobionts from such
locations may help outplanted corals survive long-term
under climate change conditions.
Role of symbionts in a sexual restoration program
An important question in sexual propagation is when
(i.e., at what age) to outplant sexual offspring. Evidence
suggests that increasing recruit size increases outplant
survivorship (Raymundo and Maypa 2004) such that an
extended grow-out period in the nursery may be worth-
while provided costs of ex situ rearing can be minimized.
For species with larvae that lack symbionts (i.e., those
that acquire symbionts via horizontal transmission), the
process of symbiont colonization during early life
deserves attention. The onset of symbiosis can be as
early as 2–6 days after fertilization (Schwarz et al. 1999,
Edmunds et al. 2005, Harii et al. 2009). In rare cases,
the association is highly specific from the outset, where
the host harbors one algal species from juvenile to adult
stages (e.g., Fungia scutaria; Weis et al. 2001). More
commonly, during early onset the association is plastic
(with the formation of partnerships sometimes involving
multiple symbiont species), but ultimately shifts to a
stable dominant species of Symbiodiniaceae during the
juvenile stage (Coffroth et al. 2001, van Oppen 2001,
Abrego et al. 2009, Cumbo et al. 2013, Yamashita et al.
2018). While colonization itself does not seem to be a
limiting step, symbiont community composition is
another major determinant (along with host genet) of
physiological performance of the coral (Little et al.
2004, Parkinson et al. 2015a, Grottoli et al. 2018) and is
expected to vary with outplant environment.
Provisioning of sexual recruits.—In the natural environ-
ment, typical Symbiodiniaceae sources for coral recruits
include the water column, sediments, and adult corals
(Coffroth et al. 2006, Adams et al. 2009, Nitschke et al.
2016, Cunning et al. 2017, Ali et al. 2018, Quigley et al.
2018). It is straightforward to provision coral juveniles
with mixtures of cultivated micro-algae when they are
kept in small aquaria ex situ, but only a subset of the
Symbiodiniaceae diversity is currently cultured. Further,
relatively little is known regarding how to provision par-
ticular symbionts, in situ,in such a way as to maximize
their uptake by coral larvae or juveniles. Environmental
conditions affect larval symbiont acquisition, with
increasing temperatures appearing to select for thermo-
tolerant symbionts, at least in Acropora from the Great
Barrier Reef (Abrego et al. 2012). One strategy to facili-
tate the acquisition of appropriate symbionts is thus to
outplant settlers prior to symbiont colonization. That
way, Symbiodiniaceae are acquired from the outplant
environment, likely promoting symbionts that are spe-
cialized for that environment (LaJeunesse et al. 2004,
2010, Abrego et al. 2012, Howells et al. 2012). However,
maturation of the symbiont community can take 1.5–
3.5 years (Abrego et al. 2009, Yamashita et al. 2013),
and does not always match that of the adult community
at the outplant site (Little et al. 2004). There is relatively
less information on the acquisition of different sym-
bionts by Caribbean scleractinian corals, but laboratory
studies suggest that an uptake window of up to
4 months exists (McIlroy and Coffroth 2017), and that
it can take up to 4 years before the community stabilizes
(Coffroth et al. 2010, Poland and Coffroth 2017). A
hybrid approach has been taken by managers and
researchers in Mexico who transfer outplants to the reef
for two weeks to take up local symbionts and then
return them to the nursery to achieve additional growth
before final outplanting (Claudia Padilla and Ania
Banaszak, personal communication). Additional research
on the optimal timing of outplanting sexual recruits is
needed.
Rare species.—Rare coral species that also associate
with rare symbionts such as the threatened Caribbean
pillar coral, Dendrogyra cylindrus and its symbiont Bre-
violum dendrogyrum (Lewis et al. 2018, Chan et al.
2019) face additional challenges. Because adult D. cylin-
drus are the only known reservoirs for this symbiont,
Article e01978; page 14 ILIANA B. BAUMS ET AL. Ecological Applications
Vol. 29, No. 8

and these populations are in rapid decline, it cannot be
assumed that natural sexual recruits will readily be able
to acquire appropriate symbionts. Consequently, larval
recruits might have to be exposed to adult conspecifics,
or special efforts made to culture these Symbiodiniaceae
specifically for restoration.
FUTURE RESEARCH NEEDS
The recommendations in this review are based on the
best available science, but knowledge gaps exist that
should be the focus of future research. In general, it has
to be recognized that nursery rearing of both larvae and
adult fragments imposes unintended selection for nurs-
ery-adapted genets (Christie et al. 2012, 2016, Morvezen
et al. 2016, Horreo et al. 2018, O’Donnell et al. 2018),
although the strength of the selection is not yet known
but could be estimated. For example, larval culturing
selects gametes and larvae that can survive netting, high-
density rearing, handling during water changes, settling
on artificial substrates, and so on. Data from other sys-
tems demonstrate that after removal of initial culture
selection, species can adapt to wild conditions rapidly,
especially if time spent in captivity is short (Espeland
et al. 2017, but see Horreo et al. 2018). Our review
already includes recommendations to reduce unintended
selection such as diversified provenancing (over different
habitats and times), intentionally promoting gene flow,
and matching the nursery and reef environments as clo-
sely as possible (Frankham 2008, Espeland et al. 2017).
Both outbreeding and inbreeding depression have yet to
be tested experimentally in corals and should be a focus
of future research. Outbreeding depression could occur
despite our expectations, especially if the number of out-
planted genets approaches the number of genets surviv-
ing in the wild. Consequences include (1) wasting
resources by transplanting maladapted genets and (2)
preventing rapid local adaptation when foreign geno-
types reproduce with local genets. We are not aware of
definitive evidence for outbreeding depression in corals,
but the topic is receiving renewed attention in marine
species (Pritchard et al. 2013, Pereira et al. 2014, Elling-
son and Krug 2016, Phillips et al. 2017). Inbreeding
depression could occur after repeated rounds of sexual
reproduction among closely related genets in a nursery
setting but that seems a far-off risk, given the challenges
of long-term coral culture and breeding combined with
relatively long generation times.
Unintended introduction of invasive pests when mov-
ing corals over large distances is another concern. This
risk is particularly relevant for corals given the dire toll
infectious disease have had on coral populations (Walton
et al. 2018) and lack of screening tools for pathogens.
Translocating larvae or gametes (i.e., cryo-preserved
sperm), when undertaking AGF, rather than adult frag-
ments, is a good option to minimize this risk (Hagedorn
et al. 2012) and further refinement of these methods is a
research priority. Basic biosecurity practices such as
visual inspections and quarantine can also reduce risk of
unintended pest introduction (IUCN/SSC 2013).
To improve the prospects for leveraging specific genets
and traits in future restoration, it is crucial to link coral
genets with phenotypic performance and fine-grain envi-
ronmental data. We call for an open-access database to
catalog all managed genets in nurseries and outplants.
This would also address a specific aim (Action 4a) in the
Endangered Species Act recovery plan for A. palmata
and A. cervicornis (NMFS 2015). Achieving this goal
will require a coordinated effort by practitioners and
researchers to report standardized metadata for each
genet in the database allowing integration with other
ongoing monitoring efforts (e.g., Atlantic and Gulf
Rapid Reef Assessment database; available online).
12
At
a minimum, the database should contain information
about the collection site (Geographical Positioning Sys-
tem coordinates), collection date, sample depth, and col-
lector information. Additional information on the
phenotypic traits and environmental variables discussed
should be collected when possible. Finally, if the budget
permits genotyping (Box 1), a clonal identification num-
ber should be assigned to genets based on the compar-
ison of their multilocus genotype (MLG) pattern against
a background of archived genotypes (for example, previ-
ously detected acroporid genomic variants; Ktichen
et al. 2019).
A way forward is the integration of the recommended
actions into a decision-making framework to decide on
how and when interventions should be made, and the
development of such a framework is another recom-
mended research priority (Anthony et al. 2015).
CONCLUSIONS
Reef restoration has made significant progress via the
development of innovative ways to grow and outplant
corals. While the task of restoring reefs in the face of
rapid climate change remains daunting and will prove
futile if current carbon emissions continue unabated,
coral species still harbor a significant amount of genetic
variation that can be leveraged to enable rapid adapta-
tion if the restoration community adopts an evolution-
centric strategy. The heterogeneity in response to stress
is what provides the hope that reef-restoration work is
worth the time and effort. We posit that this natural
heterogeneity can be capitalized upon, using the recom-
mendations herein, in a way that may speed up natural
selection and provide a means for certain species and
coral ecosystems to persist.
ACKNOWLEDGMENTS
The Coral Restoration Consortium (CRC) formed in the fall
of 2016 and established five initial working groups to provide
best management practices for coral restoration with
12
http://www.agrra.org/
December 2019 RESTORING CORAL POPULATIONS Article e01978; page 15

collaborative participation of practitioners, reef managers, and
scientists. The synthesis provided here is the first product of the
coral genetics and science working group. Thanks to S. R.
Palumbi for advising the working group. Special thanks to M.
L. Loewe for her logistical support of the working group. We
are grateful to the reviewers and editor for helping us improve
the manuscript. All authors contributed to the writing and edit-
ing of the manuscript. I. B. Baums organized the workshop and
led the writing. The CRC, the National Oceanographic and
Atmospheric Administration, the Pennsylvania State Univer-
sity’s Institute for Sustainability, Institute for Energy and the
Environment and the Center for Marine Science and Technol-
ogy are acknowledged for travel and logistics support. I. B.
Baums was supported by NSF grants OCE 1537959 and IOS
1810959. Any use of trade, firm, or product names is for
descriptive purposes only and does not imply endorsement by
the U.S. Government.
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