Marked population and phylogenetic structure are consistent with
lineage diversification in geographic isolation in Arabian mangroves
Population structure analyses recovered remarkably high levels of
divergence across Arabia, and identified groups of genetic clusters that
mirrored the geographic distribution of mangroves across the various
seas surrounding the Arabian Peninsula. A t-SNE analysis based on
selectively neutral SNPs revealed a striking, widespread pattern of
differentiation among almost all sampled populations, suggesting limited
dispersal and long-term divergence between biogeographic regions, but
also among sub-regional populations. Within the Red Sea, SNMF plots
showed a pattern of genetic differentiation that separated the
populations from the north, the center and the south of the basin into
three distinct groups. SNMF scores also showed marked genetic
differentiation between the northern and southern basins of the PAG, as
well as considerable levels of shared ancestry between the populations
of the southern PAG basin and the Sea of Oman, suggesting either
incomplete lineage sorting or ongoing gene flow.
Phylogenetic inference revealed a generalized pattern of reciprocal
monophyly among Arabian mangrove populations, and identified clearly
differentiated phylogenetic lineages occurring in the Red Sea, the
Arabian Sea and the PAG. Patterns of phylogenetic divergence among
Arabian biogeographic regions have been previously reported for other
marine taxa (34-36 ), congruent with the geographic distribution
of the species and with physical barriers to gene flow (24, 36 ).
However, few marine organisms in Arabia exhibit comparable levels of
differentiation at such fine geographic scales as the gray mangrove,
suggesting a process of genetic diversification occurring within the
historically enclosed water bodies of the Red Sea and the PAG. Neutral
population structure and phylogenetic relationships reported here
support the hypothesis of mangroves finding refuge within the enclosed
water bodies of the Arabian Peninsula during glacial cycles of the
Pleistocene, where lineages could diverge in geographic isolation.
Geological and paleoclimatic data suggest that areas of the Red Sea
basin could indeed have acted as glacial refugia for mangroves
(22 ), as it has been proposed for other marine endemic lineages
of the region (21, 24 ). This scenario is particularly striking in
the case of the PAG, where the presence of potentially suitable habitats
was arguably very limited during glacial periods, where only the estuary
of the historic Shatt-Ur river outlet to the Sea of Oman near the Strait
of Hormuz had been thought to occur (23 ). Interestingly,
populations from the southern basin of the PAG appeared as more closely
related to the populations of the Sea of Oman, on the other side of the
Strait of Hormuz, than with those of the northern PAG basin. This
sequence of cladogenetic events also better fits a scenario of
differentiation in glacial refugia where populations in the north would
have become isolated earlier as the shore lines retreated, as opposed to
a scenario of recent colonization throughout the PAG after the LGM,
where northern populations would represent the most recent phylogenetic
split (e.g. 35 ).
Demographic inference supports lineage divergence in (cryptic)
glacial refugia and limited gene flow between Red Sea populations Two analyses comparing three and six different demographic models were
run with fastSIMCOAL2 to identify the most likely scenario under which
mangroves from the Red Sea and the PAG diverged, respectively. For the
Red Sea, AIC revealed that the most likely scenario was consistent with
lineage splits occurring during a period spanning the two last glacial
cycles, suggesting that mangroves may have colonized the Red Sea basin
roughly after the Strait of Bab al-Mandab opened to the Indian Ocean ca.
400,000 years ago (22 ) and persisted thereafter. Glacial cycles
in the Red Sea are characterized by changes in the eustatic sea level
and connectivity, but also by periods of desiccation and sharp changes
in salinity and temperature. Therefore, the results reported here
suggest that the levels of population and phylogenetic diversity found
in the Red Sea are the product of historical events involving changes in
aspects of population history such as effective size and geographic
isolation, but also environmental conditions (21, 36 ). Moreover,
the model with the highest likelihood for the Red Sea revealed
relatively small effective population sizes, and no signs of recent gene
flow among populations, a pattern that was further supported by the
TreeMix analysis. This observation is unexpected as, unlike the PAG, the
Red Sea lacks potential geographic barriers. The Red Sea presents a
number of circulation features, particularly a system of meridional
eddies in the Central Red Sea (37 ) that act to create an
oceanographic discontinuity, which may limit propagule dispersal.
However, large-scale high levels of surface circulation resulting from
the Red Sea overflow and the Gulf of Aden intermediate water cells
(16, 38 ) suggest that marine currents are not limiting migration
among mangrove populations along the basin. Moreover, mathematical
models simulating mangrove propagule dispersal across the global oceans
have shown moderate to high dispersal densities for the Red Sea
(39 ).
In the case of the PAG, the model that better fit our data revealed a
scenario of simultaneous cladogenesis dating to 32,725 years, prior to
the LGM and the later infilling of the enclosed sea. These results
support the hypothesis of lineage diversification within the enclosed
water body of the PAG during a period of low sea connectivity.
Furthermore, the estimated splitting time reveals the presence of
cryptic glacial refugia within the PAG, which was nearly completely
drained during the LGM (23 ). Drastic changes in environmental
conditions during glacial maxima, particularly in terms of salinity and
temperature may have presented exceptional physiological challenges to
resident marine life. Until now, survival through glacial periods has
not been documented for any marine taxa in the PAG. However, conditions
of intertidal zones in marine swamps, while extreme, may have remained
locally suitable for gray mangroves. Lambeck (23 ) reconstructions
of historic shorelines at times of the LGM show the potential
development of lagoons and lakes in several localities, with the main
ones corresponding to what are now northern and southern basins, as well
as in the Strait of Hormuz. Indeed, today A. marina occurs in a
number of inland, non-tidal saline or even freshwater lakes (e.g.40, 41, 42 ) under conditions that could resemble those of the PAG
during glacial periods. Also, previous examples of marine cryptic
glacial refugia have been documented for taxa such as seaweeds, rays and
snails in places like southwest Ireland, the northern Brittany-Hurd Deep
area of the English Channel, the Azores islands or the northwest Iberian
Peninsula (21, 43-45 ), suggesting that the persistence of benign
local conditions in marine environments during glacial periods may be
relatively common. In addition to a split occurring prior to the last
glacial maximum, the best fitting demographic model revealed potential
gene flow between PAG basins and between the southern basin and the Sea
of Oman. The TreeMix analysis also detected significant levels of gene
flow between both terminal and ancestral branches, suggesting that some
migration could occur as mangrove populations became isolated and also
after the LGM, once the infilling of the PAG started. Potential barriers
such as the narrow waterway of the Strait of Hormuz or the marine eddies
between Qatar and Iran separating the northern and southern basin may,
therefore, not be as limiting for mangrove propagule dispersal as has
been proposed for other species (35, 46 ).
Our analyses reveal thereby a process of lineage diversification in the
mangroves of Arabia, which differentiated in geographic isolation during
glacial periods, followed by a phase of secondary contact within the
main water bodies bordering the peninsula. Although taking place before
the LGM, the Arabian mangrove system represents a strikingly fast
process of diversification, occurring at temporal scales of tens to a
few hundred thousand years. Generation time for the gray mangrove has
been estimated at 20 years in tropical areas (31, 47 ), and to
range from 25.6 to 53.8 years in high-latitude populations of the PAG
(48 ), which implies that the diversification process may date
back to as few as 12,000 generations or less. High levels of population
divergence are expected at the edge of species’ ranges, where reduced
population sizes and pronounced habitat fragmentation can lead to rapid
differentiation due to drift in isolation and divergent selection
(10 ). In addition, and despite long flotation periods during
which propagules remain viable, a relatively low dispersal capacity has
been reported for A. marina (49 ), which may also promote
genetic differentiation among peripheral populations. Indeed, higher
genetic structure in the margins of the species distribution compared to
core populations of the gray mangrove of the West Pacific has been
previously reported (50 ). Moreover, increased rates of speciation
have been documented in other mangrove systems undergoing periodic
cycles of isolation and gene flow due to fluctuations in sea level
during glacial periods (31 ), similar to what may have occurred in
the enclosed water bodies of the PAG and especially the Red Sea.
Overall, the results reported here reveal mangrove peripheral
populations as potentially important sites for speciation, and suggest
that such populations may be of particular conservation value as
significant drivers of intraspecific diversity and sources of
evolutionary innovation (10, 11 ).
Redundancy analyses reveal multi-loci adaptive divergence driven
by environmental extremes and distinct genotype-environment association
patterns in Arabian mangroves In an RDA based on population allele frequencies, four constraining
variables approximating key environmental parameters for mangrove
ecology explained 18.3% of the total variance in population SNP
frequencies. 668 SNP outliers were identified based on their
contribution to the genotype-environment association patterns. We also
identified 51 functionally annotated genes associated with one or more
SNP outliers. Among the functions associated to detected candidate
genes, at least eleven seem particularly relevant for adaptation to the
extreme and variable habitats of the seas around the Arabian Peninsula,
including regulation of responses to multiple abiotic stresses such as
drought, salinity and low and high temperature extremes; stomatal
regulation; modulation of germination, growth and flowering in response
to abiotic stresses; and Cu intake regulation and Cd tolerance (specific
relevant functional genes and further details on reported functions are
provided in the Supplementary Information).
Our genotype-environment association analysis also revealed strikingly
different patterns of covariation between genetic variance and
environmental parameters. The first two axes of the RDA based on allele
frequencies recovered highly divergent association patterns between the
Red Sea, the Arabian Sea and the PAG, yet limited variation within these
regions, as showed by the RDA scores. However, a complementary RDA based
solely on the previously identified 668 SNP outliers and computed over
individual genotypes revealed considerable adaptive divergence among Red
Sea populations (Figure 6), which differentiated along a gradient of
minimum temperatures from south to north. The Red Sea does present major
latitudinal, climatic differences along its basin. Towards the south,
strong solar insolation results in air and sea surface temperatures
exceeding the 40º and 30º C respectively, yet minimum temperatures
rarely drop under 20º C. In turn, salinity increases northwards due to
limited precipitation and high evaporation, and minimum annual air
temperatures regularly drop below 10º C, together with a reduction in
nutrient supply and productivity (17 ). As a result, the northern,
central and southern portions of the Red Sea are considered to be
distinct biotopes (15, 16, 51 ). Mangroves in these areas are
characterized by tall (> 10 m canopy height) in the
southern Red Sea, dwarf trees (< 3 m canopy height) in the
Central Red Sea, and somewhat taller (> 3 m canopy height)
mangrove trees in the northern Red Sea (17 ).
In turn, our analyses revealed reduced levels of within-group divergence
driven by environmental factors for the PAG plus the Sea of Oman
lineage. The most distal population Qurm from the Sea of Oman showed the
most divergent association signals along a gradient of salinity maxima
and to a lesser extent, of temperature minima. Remaining populations
within the clade showed limited differences, especially for those of the
PAG. Reduced divergence in patterns of genotype-environment association
may reflect less pronounced difference in habitat conditions across PAG
basins. Northern and southern PAG basins present large-scale differences
in parameters like salinity or temperature maxima and minima. However,
projections of georeferenced environmental data suggests that conditions
at the coastal, specific sites inhabited by mangroves are seemingly less
differentiated between both subregions (35, 52 ).