[Federal Register Volume 87, Number 72 (Thursday, April 14, 2022)]
[Rules and Regulations]
[Pages 22137-22141]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2022-08029]



National Oceanic and Atmospheric Administration

50 CFR Parts 223 and 226

[Docket No. 220408-0090; RTID 0648-XR119]

Endangered and Threatened Wildlife and Plants; Removal of 
Johnson's Seagrass From the Federal List of Threatened and Endangered 
Species Including the Corresponding Designated Critical Habitat

AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and 
Atmospheric Administration (NOAA), Commerce.

ACTION: Final rule.


SUMMARY: We, NMFS, are issuing a final rule to remove Johnson's 
seagrass (Halophila johnsonii) from the Federal List of Threatened and 
Endangered Species. To correspond with this action, we are also 
removing the critical habitat designation for Johnson's seagrass. These 
actions are based on newly obtained genetic data that demonstrate that 
Johnson's seagrass is not a unique taxon but rather a clone of an Indo-
Pacific species, Halophila ovalis. Therefore, Johnson's seagrass does 
not meet the statutory definition of a species

[[Page 22138]]

and does not qualify for listing under the Endangered Species Act 
(ESA). After considering public comment on the proposed rule, we are 
implementing this final rule to execute the proposed changes to the 
listing and critical habitat for Johnson's seagrass.

DATES: This final rule is effective on May 16, 2022.

Office, [email protected], (727) 209-5958.



    In 1980, a small-statured seagrass species found within Florida's 
southeastern coastal lagoon system was identified as Johnson's seagrass 
(Halophila johnsonii) (Eiseman and McMillan 1980). Prior to this 
designation, this seagrass was often referred to as H. decipiens, 
though it was most similar to the morphologically diverse Indo-Pacific 
species, H. ovalis. Morphological and physiological characteristics 
were the bases for its later taxonomic identification as H. johnsonii. 
For example, Johnson's seagrass was differentiated from other Atlantic 
Halophila species by its smooth leaf margins, angle of the cross veins 
extending from the midrib, and the lack of hairs on the blade surface 
(Eiseman and McMillan 1980).
    Given the extremely limited geographical distribution of Johnson's 
seagrass (about 200 kilometers (km) of Florida's east coast), its 
limited reproductive potential (only asexual reproduction), and the 
variety of threats that could affect survival, we conducted a status 
review in 1993 to consider whether Johnson's seagrass should be added 
to the Federal List of Threatened and Endangered Species. We published 
a proposed rule to list the species as threatened on September 15, 1993 
(58 FR 48326), and a proposed rule to designate critical habitat on 
August 4, 1994 (59 FR 39716). Additional research on the ecology of 
this species subsequently became available and was considered in an 
updated status review, which was completed in 1997. We published a 
final rule listing Johnson's seagrass as a threatened species in 1998 
(63 FR 49035, September 14, 1998) and a final rule designating critical 
habitat in 2000 (65 FR 17786, April 5, 2000).
    A peer reviewed manuscript published in October 2021 (Waycott et 
al. 2021), used a variety of genetic analyses to conclude that 
Johnson's seagrass is not a unique taxon but rather a clone of the 
Indo-Pacific species H. ovalis. In light of this new information, we 
initiated and completed a status review for H. johnsonii, which is 
documented in the proposed rule published December 23, 2021 (86 FR 
72908). Based on the best available scientific information as described 
in the proposed rule, we determined that Johnson's seagrass no longer 
meets the statutory definition of a species and therefore proposed to 
delist it under the ESA.

Basis for the Proposed Rule

    Section 3 of the ESA defines the term ``species'' as any subspecies 
of fish or wildlife or plants, and any distinct population segment of 
any species of vertebrate fish or wildlife which interbreeds when 
mature 16 U.S.C. 1532(16). Pursuant to implementing regulations in 50 
CFR 424.11(a), in determining whether a particular taxon or population 
is a species under the ESA, we rely on standard taxonomic distinctions 
as well as our biological expertise and that of the scientific 
community concerning the relevant taxonomic group.
    Under section 4(c) of the ESA, the Secretary is required to 
periodically review and revise the Federal List of Endangered and 
Threatened Species and consider, among other things, whether a species' 
listing status should be changed, including whether the species should 
be removed from the list (16 U.S.C. 1533(c)). Pursuant to implementing 
regulations for the ESA at 50 CFR 424.11(e), the Secretary shall delist 
a species if, after conducting a status review based on the best 
scientific and commercial data available, the Secretary determines: (1) 
The species is extinct; (2) the species does not meet the definition of 
an endangered species or threatened species; or (3) the listed entity 
does not meet the statutory definition of a species. When conducting a 
status review, if we determine the entity under review does not meet 
the statutory definition of a species, the status review concludes 
without further evaluation, because we can only list entities that 
qualify as species under the ESA.
    The entity described as Johnson's seagrass grows in a variety of 
conditions within Florida's intracoastal waters from Sebastian Inlet to 
Virginia Key in Biscayne Bay. This is the smallest geographic 
distribution of any seagrass worldwide. Within this range, it is among 
the least abundant seagrass. It grows in small, sparse patches and may 
disappear from areas for months or years before reappearing. It can co-
occur with other seagrasses, but its short stature precludes it from 
occurring within dense stands of taller species because it is 
outcompeted for light resources. Johnson's seagrass has a broader 
tolerance range for light, temperature, and salinity than congeners and 
seems capable of growing in suboptimal conditions where other species 
cannot survive. Johnson's seagrass grows in the intertidal zone, on 
dynamic flood deltas inside ocean inlets, at the mouths of freshwater 
discharge canals, and subtidal waters to depths of approximately 3-4 
    Johnson's seagrass is dioecious, meaning each plant only contains 
the flowers of one sex (male or female). Interestingly, no individual 
Johnson's seagrass plants have been found with male flowers. Similarly, 
researchers have not found any seedlings. These observations suggest 
that Johnson's seagrass reproduces only through vegetative 
fragmentation (asexual reproduction) and not through the development 
and dispersal of seeds (sexual reproduction). This strategy likely 
hinders its ability to expand in range and may slow recolonization 
following disturbances.
    At the time of listing, the best available data indicated Johnson's 
seagrass: (1) Had perhaps the smallest geographic range of any seagrass 
species worldwide; (2) had a sparse, patchy distribution throughout its 
range and an ability to survive in a variety of environmental 
conditions; (3) lacked male flowers necessary for sexual reproduction 
and therefore appeared to only reproduce asexually; and (4) was unique 
from other North American Halophila species based on morphology, 
physiological ecology, and genetic analyses. However, the unique life 
history and ecology of this seagrass raised questions about its 
phylogeny (history of the evolution of a species or group, including 
relatedness within a group). The 1997 status review indicated that more 
detailed studies were necessary to evaluate the overall genetic 
structure and diversity of H. johnsonii. This need was reiterated in 
the 2002 Johnson's Seagrass Recovery Plan.
    A 1997 genetics study using randomly amplified primer DNA-
polymerase chain reactions (RAPD-PCR) indicated that genetic diversity 
was higher than expected at one location within the range of Johnson's 
seagrass (Jewitt-Smith et al. 1997). Yet this study relied on a limited 
sample size, and a subsequent study using similar techniques indicated 
very low genetic diversity within H. johnsonii as compared to the co-
occurring species, H. decipiens (Freshwater 1999). The low genetic 
diversity was attributed to the lack of sexual reproduction. The

[[Page 22139]]

methodology used in assessing these Halophila samples did not provide 
the resolution necessary to make species level conclusions about 
    A molecular phylogenetic analysis of the genus Halophila using 
internal transcribed spacer (ITS) regions of nuclear ribosomal DNA 
indicated that H. johnsonii could not be distinguished from H. ovalis 
and should be further researched (Waycott et al. 2002). Umichura (2008) 
came to a similar conclusion and suggested that H. johnsonii and two 
other Halophila species should be reclassified as the broadly 
distributed H. ovalis. Short et al. (2010) used ITS regions of nuclear 
ribosomal sequences and morphology to demonstrate that Halophila 
samples from Antigua belonged to H. ovalis and were genetically 
identical to H. johnsonii. Short et al. (2010) also found that 
Halophila samples from both Antigua and the United States (the latter 
of which were previously identified as H. johnsonii) fell within the 
range of morphological characteristics diagnostic for H. ovalis, and 
particularly for H. ovalis from east Africa. The outcomes of these 
studies raised more questions about the taxonomy of Halophila species, 
particularly H. johnsonii, given its unusually restricted geographic 
range, its limited reproductive strategy, and its morphometric 
similarities to other Indo-Pacific species of Halophila.
    NMFS began funding projects to resolve the taxonomic uncertainty of 
Johnson's seagrass in 2012. Waycott et al. (2015) used multiple genetic 
approaches including microsatellite DNA and next generation sequencing 
to detect single nucleotide polymorphisms (SNPs). Results of this work 
indicated a complete lack of genetic diversity across the range of 
Johnson's seagrass and through time, indicating all samples analyzed 
were from a singular clone. Samples collected and analyzed from Antigua 
contained the same genetic markers as samples from Florida, suggesting 
these too were part of the same clone (Waycott et al. 2015) despite the 
Antigua samples having been previously identified as H. ovalis (Short 
et al. 2010). Finally, Waycott et al. (2015) genetically compared 
samples from both Florida and Antigua with H. ovalis samples collected 
throughout that species' range (Indo-Pacific). Results indicated all 
samples, regardless of location or identification, had allelic overlap 
(same gene variations) at 6 of 10 microsatellite loci analyzed, 
suggesting samples from the Atlantic originated from H. ovalis of the 
Indo-Pacific. While this report provided further evidence that H. 
johnsonii was not a unique taxon, SNP locations for H. ovalis had yet 
to be verified for H. johnsonii samples and the report did not present 
a comprehensive population genetic analysis of H. ovalis.
    NMFS provided support for a follow-up study in 2017, recently 
published as Waycott et al. (2021). This study expanded previous 
efforts with the intent of solidifying the methods and providing a 
robust conclusion regarding the taxonomic uncertainty within the H. 
ovalis complex. The study used multiple methodological approaches and 
created molecular data sets for samples of both H. johnsonii and H. 
ovalis collected throughout the range of each species. Phylogenetic 
analyses of 105 samples of Halophila spp. from 19 countries using 
plastid (17,999 base pairs (bp)) and nuclear (6,449 bp) DNA sequences 
derived from hybrid capture both resolved H. johnsonii within H. 
ovalis. A third phylogenetic analysis using 48 samples from 13 
populations identified 990 genome-wide SNPs (generated via double 
digest restriction-site associated digest sequencing (ddRAD)) and also 
nested H. johnsonii within H. ovalis. All three phylogenetic analyses 
indicated H. johnsonii samples were most similar to H. ovalis samples 
from Antigua and east Africa.
    Waycott et al. (2021) also assessed population-level differences 
using both the genome-wide SNPs (990) developed in the phylogenetic 
analysis (47 of the 48 samples from 13 populations) and microsatellites 
(294 samples at 10 microsatellite loci). Cluster analysis indicated 
three populations within the H. ovalis complex, with H. johnsonii being 
part of the Indo-Pacific/Atlantic clade. Other results demonstrated 
genetic uniformity of all 132 H. johnsonii samples, indicating a 
complete lack of genetic diversity that is consistent with clonal 
(asexual) reproduction and a single colonization event. These same 132 
samples and the 12 H. ovalis samples from Antigua shared a single 
multilocus genotype at all nine comparable microsatellite loci. 
Furthermore, all 12 H. johnsonii samples and the single H. ovalis 
sample from Antigua genotyped with ddRAD loci shared the same 
multilocus genotype. In contrast, other H. ovalis populations, such as 
those from Australia, generally had multiple multilocus genotypes and 
substantial genetic diversity, indicating that the genetic markers 
would have detected differences if they were present. The population-
level analyses indicate that H. johnsonii is genetically 
indistinguishable from H. ovalis, clustering with samples from Antigua 
and east Africa.
    Collectively, the Waycott et al. (2021) study concluded that the 
entire range of H. johnsonii is a single clone of a morphological 
variant of the Indo-Pacific species H. ovalis. After reviewing the best 
information available, we agree that H. johnsonii should be synonomized 
with H. ovalis and not considered a separate taxonomic species. It 
cannot qualify as a distinct population segment (DPS) under the 
statutory definition of a species because DPSs can be identified only 
for vertebrate fish or wildlife, not plants. Therefore, H. johnsonii 
does not meet the statutory definition of a species under the ESA, and 
on that basis, we published a proposed rule on December 23, 2021, to 
remove Johnson's seagrass from the Federal List of Threatened and 
Endangered Species and to remove its corresponding critical habitat 
from 50 CFR part 226 (86 FR 72908).

Public Comment

    Upon publication of the proposed rule, we solicited comments during 
a 60-day public comment period from all interested parties. We received 
nine comments, two of which were nearly identical. Summaries of the 
comments received and our responses are provided in the following 
    Comment 1: Four commenters supported the proposed delisting based 
on the information provided in the proposed rule.
    Response: We thank these commenters for their support of the 
proposed delisting.
    Comment 2: Two commenters disagreed with the proposed delisting on 
the basis of the need to continue to protect all seagrasses and 
seagrass habitats given the unique ecosystem functions they provide. 
One of these commenters recognized our finding that H. johnsonii is not 
a species eligible for listing because it is a clone of H. ovalis, but 
suggested that H. ovalis found in Florida should be listed given the 
ongoing threats it faces there.
    Response: While we agree with the commenters that seagrasses serve 
a critical ecosystem function by, for example, stabilizing substrate 
and providing both forage and habitat for a variety of species, the 
best scientific information available indicates that this seagrass is 
not a unique taxon but rather a clone of the Indo-Pacific species H. 
ovalis. Synonymizing H. johnsonii with H. ovalis means the entity 
currently listed under the ESA as Johnson's seagrass is not a taxonomic 
species, and is therefore not eligible for listing under the ESA. H. 
ovalis could be considered for future listing under the ESA. However, 
that would require a separate

[[Page 22140]]

review to consider the status of that species throughout the entirety 
or a significant portion of its range. At that time, we would be able 
to evaluate whether the species is eligible for and should be listed 
because of any of the threats it faces in waters off Florida.
    We agree with the importance of seagrasses to the environments in 
which they are found. Though delisting H. johnsonii from the ESA 
removes the protections of the ESA for this ``species'' and its 
critical habitat, NMFS will continue to support seagrass conservation 
under other statutory authorities. For example, the South Atlantic 
Fishery Management Council has identified seagrass and habitats 
containing seagrasses as essential fish habitat (EFH) for certain 
federally-managed fish species in the South Altantic, such as snapper 
and grouper, under the Magnuson-Stevens Fishery Conservation and 
Management Act (MSA). EFH is defined as ``those waters and substrate 
necessary to fish for spawning, breeding, feeding, or growth to 
maturity.'' 16 U.S.C. 1802(10). As required under the MSA, federal 
agencies (e.g., U.S. Army Corps of Engineers) consult with NMFS on any 
action that may adversely affect EFH 16 U.S.C. 1855(b)(2). NMFS 
provides comments and EFH Conservation Recommendations for those 
actions that affect EFH and those recommendations can include measures 
to ensure federal projects avoid, minimize, and, if necessary, mitigate 
impacts to EFH as a means to conserve and promote sustainable 
fisheries. 16 U.S.C. 1855(b)(4); 50 CFR 600.905(b), 600.920, and 
600.925. The delisting under the ESA does not affect the mechanisms to 
conserve and protect seagrasses as EFH under the Magnuson-Stevens 
Fishery Conservation and Management Act.
    Comment 3: One commenter agreed with the agency's rationale for 
delisting this seagrass but recommended further consideration for 
retaining the critical habitat designation as a means of overall 
ecosystem conservation.
    Response: Critical habitat can only be designated for species on 
the Federal List of Threatened and Endangered Species (16 U.S.C. 
1532(5), 16 U.S.C. 1533(a)(3)). Therefore, the Johnson's seagrass 
critical habitat designation cannot be retained when the species is 
removed from the List.
    Comment 4: One commenter agreed with the agency's rationale for 
delisting Johnson's seagrass but expressed concern that removal from 
the list could adversely affect other seagrasses that co-occupy habitat 
in that region.
    Response: As discussed previously, NMFS agrees with the importance 
of seagrasses and their habitats and will continue to promote 
conservation through the MSA (see response to Comment 2).

Summary of Changes From Proposed Rule

    We evaluated whether any pertinent scientific or commercial 
information became available since publication of the proposed rule. We 
reviewed the best available scientific and commercial information, 
including all public comments. Based on all available information, we 
have made no changes from the proposed rule.

Final Determination and Effects of Determination

    As proposed on December 23, 2021 (86 FR 72908), and concluded with 
this final rule, we remove H. johnsonii from the Federal List of 
Threatened and Endangered Species because the best available scientific 
and commercial data indicate that the listed entity is synonymous with 
H. ovalis and does not meet the statutory definition of a species. 
Because critical habitat can only be designated for species listed 
under the ESA, we also remove the designated critical habitat for H. 
johnsonii. As of the effective date, the protections of the ESA will no 
longer apply to H. johnsonii. However, the delisting of H. johnsonii 
and removal of the designated critical habitat are specific to the ESA 
and will have no effect on other Federal, state, county, or local 
seagrass protections that may be in place. In addition, because H. 
ovalis is not listed as an endangered species or threatened species 
under the ESA, our delisting of H. johnsonii will have no effect on the 
status of H. ovalis.
    Per the joint NMFS-U.S. Fish and Wildlife Service Post-Delisting 
Monitoring Plan Guidance (2008, updated in 2018), the post-delisting 
monitoring requirements of section 4(g) of the ESA apply without 
exception to all species delisted due to biological recovery, but do 
not pertain to species delisted for other reasons, such as taxonomic 
revision. Based on this reasoning, there is no need for a post-
delisting monitoring plan for H. johnsonii.

References Cited

    The complete citations for the references used in this document can 
be obtained by contacting NMFS (See ADDRESSES and FOR FURTHER 

Information Quality Act and Peer Review

    In December 2004, the Office of Management and Budget (OMB) issued 
a Final Information Quality Bulletin for Peer Review establishing 
minimum peer review standards, a transparent process for public 
disclosure of peer review planning, and opportunities for public 
participation. The OMB Peer Review Bulletin, implemented under the 
Information Quality Act (Pub. L. 106-554), is intended to enhance the 
quality and credibility of the Federal Government's scientific 
information, and applies to influential or highly influential 
scientific information disseminated on or after June 16, 2005.
    To satisfy the requirements under the OMB Peer Review Bulletin, the 
Waycott et al. (2021) manuscript was subjected to peer review in 
accordance with the Bulletin. Our proposed action relies upon new 
information within the manuscript, which we consider ``influential 
scientific information.'' While the manuscript was published in the 
peer-reviewed journal Frontiers in Marine Science, and peer reviewed by 
that journal prior to publication, we also peer reviewed the 
manuscript. We established a peer review plan that consisted of 
subjecting the manuscript to review by a panel of four expert reviewers 
identified by NOAA's Genetics Group. The peer review plan, which 
included the charge statement to the peer reviewers, and the resulting 
peer review report are posted on the NOAA peer review agenda at: 
https://www.noaa.gov/organization/information-technology/peer-review-plans. In meeting the OMB Peer Review Bulletin requirements, we have 
also satisfied the requirements of the 1994 joint U.S. Fish and 
Wildlife Service and NMFS peer review policy (59 FR 34270, July 1, 


National Environmental Policy Act (NEPA)

    The 1982 amendments to the ESA, in section 4(b)(1)(A), restrict the 
information that may be considered when assessing species for listing 
to the best scientific and commercial data available. Based on this 
limitation of criteria for a listing decision and the opinion in 
Pacific Legal Foundation v. Andrus, 657 F. 2d 829 (6th Cir. 1981), we 
have concluded that NEPA does not apply to ESA listing actions. (See 
NOAA Administrative Order 216-6A and the Companion Manual for NOAA 
Administrative Order 216-6A, regarding Policy and Procedures for 

[[Page 22141]]

with the National Environmental Policy Act and Related Authorities.)

Executive Order 12866, Regulatory Flexibility Act, and Paperwork 
Reduction Act

    As noted in the Conference Report on the 1982 amendments to the 
ESA, economic impacts cannot be considered when assessing the status of 
a species. Therefore, the economic analysis requirements of the 
Regulatory Flexibility Act are not applicable to the listing process. 
In addition, this final rule is exempt from review under Executive 
Order 12866. This final rule does not contain a collection of 
information requirement for the purposes of the Paperwork Reduction 

Executive Order 13132, Federalism

    E.O. 13132 requires agencies to take into account any federalism 
impacts of regulations under development. It includes specific 
consultation directives for situations where a regulation will preempt 
state and local law, or impose substantial direct compliance costs on 
state and local governments (unless required by statute). Neither of 
these circumstances is applicable to this final rule.

List of Subjects

50 CFR Part 223

    Endangered and threatened species.

50 CFR Part 226

    Endangered and threatened species.

    Dated: April 11, 2022.
Samuel D. Rauch, III,
Deputy Assistant Administrator for Regulatory Programs, National Marine 
Fisheries Service.

    For the reasons set out in the preamble, 50 CFR parts 223 and 226 
are amended as follows:


1. The authority citation for part 223 continues to read as follows:

    Authority:  16 U.S.C. 1531 1543; subpart B, Sec.  223.201-202 
also issued under 16 U.S.C. 1361 et seq.; 16 U.S.C. 5503(d) for 
Sec.  223.206(d)(9).

Sec.  223.102   [Amended]

2. In Sec.  223.102, in the table in paragraph (e), remove the 
undesiganted heading ``Marine Plants'' and the entry for ``Seagrass, 


3. The authority citation for part 226 continues to read as follows:

    Authority:  16 U.S.C. 1533.

Sec.  226.213   [Removed and Reserved]

4. Remove and reserve Sec.  226.213.

[FR Doc. 2022-08029 Filed 4-13-22; 8:45 am]