Introduction
Understanding the roles of environment and geography in the process of
evolutionary divergence is essential to understand the mechanisms
underlying the early stages of speciation. Evolutionary divergence may
result from the accumulation of genetic differences caused by drift in
geographic isolation, a mode of divergence driven by neutral factors
(1, 2 ). In turn, geographic variation in environmental conditions
can result in divergent selection, the diversifying process that drives
ecological speciation (3 ). In ecological speciation models,
reproductive barriers arise as a by-product of cumulative, ecologically
adaptive changes (4, 5 ), enabling genome‐wide differentiation at
both neutral and selected loci through isolation-by-adaptation (IBA;3 ). Ecological speciation in geographic isolation is
theoretically uncontroversial, and deemed common in nature as a
mechanism maintaining lineage diversity upon secondary contact (3,
5 ). However, whether ecological speciation in the absence of geographic
isolation and reduced gene flow occurs frequently in nature remains
questioned in evolutionary research (6, 7 ). The interactions
between selection and the stochastic effects derived from processes such
as founder events, bottlenecks and genetic drift also remain poorly
understood, and difficult to assess in natural systems (8, 9 ).
Biological systems occurring in the environmentally heterogeneous and
often extreme habitats at species’ range edges are suitable models to
investigate questions related to evolution. The environment at the edges
of species’ range tends to be stressful and spatially discontinuous, as
well as temporally unstable (10 ), frequently resulting in dynamic
settings of multiple isolated populations subject to strong differential
selection. The severe and stochastic character of peripheral
environments is hypothesized to generate strong selective interplay
between adaptation and neutral processes (11 ), providing an ideal
opportunity for speciation research. One of such systems is provided by
gray mangrove populations in the Arabian Peninsula (Avicennia
marina var. marina ). The gray mangrove has the broadest
distribution of any mangrove species, extending across the Indian Ocean
and into the West Pacific as far as Japan and New Zealand (12 ).
The Arabian Peninsula represents one of the northernmost edges of the
species’ distribution, as well as a stressful habitat characterized by
extreme temperatures, aridity, and often extreme salinity, factors known
to be limiting for mangrove growth (13-15 ). Arabian marine
domains are also environmentally diverse both within, and between, the
main water bodies bordering the peninsula, which define three main
biogeographic regions: (i) the Red Sea, where the marine system presents
opposing gradients of salinity and temperature, with the highest
temperature and lowest salinity values occurring in the shallow southern
basin, while the north has cooler temperatures but high salinity as a
result of limited precipitation and high evaporation (16, 17 );
(ii) the Persian/Arabian Gulf (referred to as ‘PAG’ hereafter) to the
northeast of the Arabian Peninsula, where populations are subject to
arid (<250 mm) to hyper-arid (<100 mm) rainfall
regimes, and experience the widest range of air temperatures in the
region throughout the year, with temperatures varying from 2 °C to 48 °C
in specific coastal sites (18, 19 ); and (iii) the Arabian Sea,
which in contrast with former biogeographic regions, has normal oceanic
salinity, and summer temperatures that are buffered by cold-water
upwelling as a result of the Indian Ocean monsoon, resulting in more
moderate environmental conditions (20 ).
The Arabian Peninsula has experienced large fluctuations in
environmental conditions throughout glacio-eustatic cycles that largely
impacted the biodiversity of the region, in particular for the enclosed
water bodies of the Red Sea and the PAG (21 ). Throughout the last
400,000 years, the Red Sea remained connected to the Gulf of Aden, yet
cross-sectional areas along the Strait of Bab al Mandab connecting them
were, at times of glacial maxima, as low as 2% of that today, resulting
in major increases in salinity and temperature within the Red Sea
(22 ). For several sustained periods during the last two glacial
cycles, the minimum channel widths connecting the Red Sea to the Arabian
Sea were less than 4 km wide and remained narrow whenever the local sea
levels were 50 meters below the current ones (22 ). In contrast,
models show that the PAG was nearly completely drained during the peak
of the last glaciation until c.a. 14,000 years ago, when a waterway
opened in the Strait of Hormuz (23 ). The marine incursion into
the southern PAG basin started approximately 12,500 years ago, and the
northern basin flooded ca. 1,000 years later. The present PAG shorelines
were reached just 6,000 years ago (23 ). As an open ocean habitat,
the Arabian Sea coast has only experienced vertical migration of sea
levels during these glacial periods, without geographic isolation.
The combination of extreme environmental conditions, differential
changes in habitat and dynamic barriers to gene flow, makes the seas
bordering the Arabian Peninsula one of the most variable marine
environments in the world, with a high potential for speciation driven
by both neutral and selective factors (24 ). Although the
phylogenetic relationships for the varieties of A. marina and
congeneric species have been reported for other regions (25, 26 ),
the extensive gray mangrove populations from the Arabian coasts have
rarely been included in reported DNA sequence-based analyses (see25, 26, 27 ). The specific drivers and molecular basis of local
adaptation and lineage diversification in A. marina remain
understudied both in Arabia and across its entire distribution.
Here, we used the Arabian gray mangrove complex to examine how extreme
habitat conditions and heterogeneous spatial settings have shaped
genetic diversity at the highly variable edge of the species’ range
using whole genome and georeferenced environmental data. First, we
analyzed patterns of population structure and reconstructed the
evolutionary and demographic history of the species in the Arabian
Peninsula. Two general competing hypotheses about the evolutionary
history of the Arabian mangroves were tested in this study: (i)
mangroves from the Red Sea and PAG were extirpated during the glacial
cycles of the Pleistocene, followed by a recolonization after the last
glacial maximum (LGM); and (ii) mangroves remained within the enclosed
seas in glacial refugia during glacial periods, and expanded once sea
levels rose. Second, we studied patterns of adaptive variability
applying genotype-environment association (GEA) analysis. We used
redundancy analysis combining environmental and single nucleotide
polymorphisms (SNP) data to survey the genome and jointly identify
environmental variables and functional genes potentially involved in
local adaptation and lineage divergence.