Biogeographic pattern in benthic community composition

The observed differences in benthic community composition among geographic zones found in this study is consistent with previous authors that have documented the biogeographic distribution of reef-building corals (McClanahan et al. 2014, Obura 2012).

The south zone had a higher LCC with most genera occurring in abundance but mainly dominated by Porites and Acropora. This area is known to have a high diversity of corals mainly due to its proximity to the WIO center of biodiversity which has been documented to be around the northern Mozambique channel (NMC) (McClanahan et al.

2014, Obura 2012). The south zone is the receiving point of coral larvae into Kenyan waters as currents transporting larvae progress northwards (Gamoyo et al. 2019) resulting in higher coral diversity compared to the north. In the north, a smaller number of genera was found with Porites being dominant, indicating a marginal coral community as it is farther from sources of larvae. The north zone is also an area of poor reef development due to the unfavorable conditions caused by the convergence of the colder nutrient rich SC and the EACC, which diminishes chances of high coral diversity in this zone. This convergence of currents makes the north an area of biogeographic transition

23 from southern East African reef communities to Somali-Arabian Gulf communities to the north. This may mean that the north zone can act as an environmental corridor for species movements as the climate warms as has been suggested for other marginal communities (McClanahan et al. 2014). Other studies have reported low coral diversity on marginal reefs e.g. upwelling reefs of the Arabian gulf (Riegl 1999), but there is also some isolated cases of high coral cover and diversity in marginal reefs e.g., at the world’s southern-most coral reefs in subtropical Islands of the Pacific Ocean (Harriott et al. 1995, Adjeroud et al.

2016). Some of these marginal reefs have the potential to act as habitable spaces for corals as climate warms, creating climate refugia or ‘seed banks’ that can re-populate coral communities once climate stabilizes to favorable conditions (Beger et al. 2014).

The benthic communities in the north and south represent two alternate aspects of coral reef resilience. The comparably lower abundance of juvenile coral colonies in the north and comparably higher abundance of large colonies suggests poor coral recruitment but high survival of adult coral colonies. Low recruitment could be attributed to isolation of the north zone from the southern sources of larvae, with only local sources of larvae for recruitment. Higher abundance of large colonies in the north may be due to the coral community in the north being protected from bleaching mortality by the cooling effect of upwellings in the SC. On the other hand, higher abundance of juvenile corals in the south indicates high recruitment likely due to its proximity to sources of larvae (Gamoyo et al. 2019, Obura 2012). The low abundance of large colonies in the south implies low survival and only a few coral colonies surviving to large sizes. The south zone is known to face more stress from bleaching as it is closer to the warmest zones at 10-12

oS, and higher anthropogenic pressures due to higher human population densities as

24 compared to the north. There have been several bleaching episodes since the 1998/99 mass coral bleaching which could have slowed down recovery of coral communities in the south.

Other studies in the WIO region have shown that the coral community in the north is very different from that in the south, with a higher diversity in the south comprising species more closely resembling the northern Tanzanian coral community (Ateweberhan

& McClanahan 2016, Obura 2012). Studies from other regions have also shown that the latitudinal gradient drives differences in benthic community composition on coral reefs.

Coral reefs in the Hawaiian Archipelago in the north Pacific Ocean show a latitudinal gradient contributing to three distinct reef regimes each dominated by either hard coral, turf algae or macroalgae (Jouffray et al. 2015). In a Caribbean-wide study, spatial and temporal differences in coral cover and macroalgae were found between subregions (Schutte et al 2010). Eastern Australia coral reefs showed a trend of decreasing cover of Acroporidae as latitude increased. The diversity of benthic communities differed along the latitudinal gradient and across geographic zones in Taiwan (Ribas-Deulofeu et al. 2016).

2.4.2 Influence of habitat factors and management on benthic community composition

Habitat factors and management influenced the pattern of benthic communities within each geographic zone. This offers the opportunity to propose ecological controls that structure benthic communities at this scale, and which may be used to guide resource management decisions. Similar findings have been reported in parts of the Pacific Ocean, where benthic communities were structured by depth, exposure to waves and reef types,

25 in the Hawaiian Islands (Jokiel et al. 2004, Jouffray et al. 2015, Vroom & Braun 2010, Williams et al. 2013) and in French Polynesia (Adjeroud 1997, Adjeroud et al. 2019, Adjeroud et al. 2016, Fajemila et al. 2015, Pante et al. 2006, Penin et al. 2007).

The heterogeneity and uniqueness of habitat types in the north of Kenya can be attributed to a number of factors including the that it is composed of a set of small islands in an archipelago, presenting diverse reef types at different depths. Perpendicular to the shore, in a cross-shelf line, there are numerous channel reefs between the islands and mainland, then lagoons, fringing reefs and at the outermost edge, a deep ridge with patch reefs on it. In addition, the northern part of Kenya has been described as an ‘ecotone’

zone due to the presence of marginal/transitional coral reef communities composed of rare or regional endemic species (Obura 2012). Other studies have also shown significant differences in benthic communities within archipelagos such as distinct coral species assemblages among different islands in Penghu in Taiwan (Hsieh et al. 2016), a cross-shelf difference in benthic community within the Spermonde Archipelago in the Coral Triangle (Teichberg et al. 2018) and differences in benthic communities across habitats in the Abrolhos archipelago of eastern Brazil (Francini-Filho 2013).

The habitat type DEPR that was uniquely found in the north zone is dominated by coralline algae, which may be due to a high biomass of fish on the patch reefs (Church &

Obura 2004, Obura 2002). Fish herbivores graze away competitors of crustose coralline algae, and fish predators feed on sea urchins which are the greatest eroders of coralline algae (O'Leary & McClanahan 2010). Also, the upwelling currents in this zone could be a source of nutrients stimulating growth of coralline algae. Previous studies have associated coralline algae as a suitable cue for coral settlement and recruitment (Bak

26 1976, O’Leary et al. 2012) making these habitats potential spaces for corals to grow.

Being deep habitats in an area of upwelling-cooler waters could offer an ecological refugia to coral communities as the climate warms (Smith et al. 2017). However, light limitation would reduce the opportunity of a diverse coral community growing and dominating these spaces (Abrego et al. 2012, Grottoli & Wellington 1999, Wethey & Porter 1976) and only a few taxa that can tolerate these depths would colonise this habitat.

A majority of deep- fringing reefs that are exposed to oceanic waves in the central and north zones were dominated by Acropora, soft corals and small-sized coral colonies (DEFU habitat type). This habitat type is characterized by gradual slopes on the fringing reefs creating an environment where Acropora can dominate competitively. Other studies have reported Acropora occupying similar environments of forereef areas, where there is low stress from sedimentation and high rates of development processes such as reproduction (Kojis and Quinn 1984). Notably, the low abundance of large colonies within this habitat is worrying considering that the south zone is an area of high coral diversity.

This could be indicative of failure to replenish standing stocks of large colonies in the central and south zone, likely due to bleaching mortality which has been recurrent over the past two decades (McClanahan 2014, Obura et al. 2017). All zones were badly affected by the 1997/98 mass coral bleaching episode with a 50 % - 80 % average loss of coral cover with some individual sites loosing up to 100 % cover (McClanahan et al.

1998, Obura 2002). Recovery has been slow since then perhaps due to the occurrence of smaller-scale bleaching episodes in 2005, 2007, 2010 and 2016 (McClanahan 2014, McClanahan 2008, Obura et al. 2017). In the south zone, this bleaching impact was likely compounded by other anthropogenic stresses originating from its high human settlement.

27 A similar explanation goes for the central zone reef where this study found few large colonies likely due to a slowed down recovery from the mass coral bleaching. Post-bleaching reports indicate that there was an increase in macroalgae and a decrease in fish biomass followed by an explosion in sea urchin density probably as a response to the decrease of fish biomass which constitute their predators. Consequently, sea urchin grazed the reef substate to bare (McClanahan et al. 1998). The presence of poor water conditions due to proximity to river Sabaki effluents, high fishing pressure and recurrent bleaching episodes could have made perseverance of coral colonies to large sizes a great challenge (Lambo & Ormond 2006, McClanahan et al. 2008).

Shallow fringing or lagoon reefs in the north and central zones (SFLPR habitat type) were characterized by a dominance of macroalgae and turf algae. Most of these habitats are proximal to land and are highly influenced by land-use activities such as effluents from rivers as well as fishing. When hard corals die macroalgae and turf algae take over the space due to increased nutrient availability or reduced herbivory (Barott et al. 2009, Litter et al 2006, McCook et al. 2001). Turf algae are the main focus of grazing but their form allows for rapid regrowth (Steneck & Dethier 1994) making them thrive even in protected areas where grazing is high. Other studies have found that macroalgae are not influenced by latitudinal effects, with more local-scale influences such as nutrient levels strongly driving their distribution (Smith et al. 2015). In this study, the abundance of macroalgae within these habitats indicates a worrying level of coral reef degradation since most coral cover and taxonomic diversity has always been thought to occur within shallow depths (Jackson et al. 1991, Lirman et al. 2003, Pandolfi 2002).

28 Shallow habitats on patch or channel reefs (SPC) were dominated by large colonies with an abundance of Porites and Echinopora. Similar observations were made in the Great Barrier Reef where large colonies of Porites were associated with shallow inshore reefs (Done 1982). The presence of large coral colonies in shallow reefs indicates a habitat type that supports the survival of corals probably due to acclimatization to bleaching (Coles & Brown 2003). Also, the high fluctuation of water temperatures in shallow reefs creates a variable environment that may support different coral genotypes.

A diversity of genotypes offers a chance for coral colonies to survive to larger sizes and persist over time as seen in an inshore reef of the Great Barrier Reef where Porites dominated through very persistent genotypes (Potts et al. 1985). In addition, Porites and Echinopora have been considered as resistant and generalist coral genera within the functional groups of corals, based on their response to bleaching (Darling et al. 2012).

This makes them capable of inhabiting shallow areas where competitive but less tolerant corals cannot survive the fluctuating temperatures, bleaching events and proximity to human disturbance such as sedimentation.

Porites is a widespread genus that occurs at different habitats and thus reinforces its functional role as a resistant species (Obura 1995, Obura 2001, Darling et al. 2012).

The presence of very large colonies of Porites in the north compared to the south could imply that bleaching mortality of Porites is lower in the north due to the presence of habitat types that support resistance properties for that genus. In the south zone, the high % cover of Porites is mainly composed of small colonies. This signifies an area which could be facing high bleaching mortality, as evidenced by high % cover of dead standing corals, but experiences high recruitment that recovers the standing stock. This recovery feature

29 may not be present in the north because Acropora communities failed to recover after the 1998 coral bleaching episode and recruitment is persistently low (Church & Obura 2004).