Some considerations when comparing SABAP 1 with SABAP 2 data

Jouanin's Petrel Bulweria fallax mainly occurs in the western Indian Ocean. Prior to our study there were only two records from east of 82° E. We show that small numbers of Jouanin's Petrels are regular visitors to the eastern Indian Ocean, occurring to 15° N 90° E in the Bay of Bengal and 15° S 123° E off northern Australia. Although seasonal coverage is limited, they have been recorded east of 80° E from April–July and October–December, but not in February–March. Most sightings are from oceanic waters at least 20 km offshore where depths exceed 500 m.     

Movement ecology of black marlin Istiompax indica in the Western Indian Ocean

The black marlin Istiompax indica is an apex marine predator and is susceptible to overfishing. The movement ecology of the species remains poorly known, particularly within the Indian Ocean, which has hampered assessment of their conservation status and fisheries management requirements. Here, we used pop-up archival satellite tags to track I. indica movement and examine their dispersal. Forty-nine tags were deployed off Kenya during both the north-east (November–April) and south-west (August–September) monsoon seasons, providing locations from every month of the year. Individual I. indica were highly mobile and track distance correlated with the duration of tag attachment. Mean track duration was 38 days and mean track distance was >1800 km. Individuals dispersed in several directions: north-east into Somalian waters and up to northern Oman, east towards the Seychelles, and south into the Mozambique Channel. Their core habitat shifted seasonally and overlapped with areas of high productivity off Kenya, Somalia and Oman during the first half of the year. A second annual aggregation off the Kenyan coast, during August and September, did not coincide with high chlorophyll-a (chl-a) concentrations or thermal fronts, and the drivers of the species' presence and movement from this second aggregation was unclear. We tested their habitat preferences by comparing environmental conditions at track locations to the conditions at locations along simulated tracks based on the empirical data. Observed I. indica preferred cooler water with higher chl-a concentrations and stayed closer to the coast than simulated tracks. The rapid and extensive dispersal of I. indica from Kenya suggests that there is likely a single stock in the Western Indian Ocean, with individuals swimming between areas of high commercial catches off northern Somalia and Oman, and artisanal and recreational fisheries catches throughout East Africa and Mozambique.     

Abundance,diversity and geographic distribution of cassava mosaic disease pandemic‐associated Bemisia tabaci in Tanzania

Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae), one of the most economically important agricultural pests worldwide, is the vector of cassava mosaic geminiviruses that cause cassava mosaic disease (CMD). In East and Central Africa, a severe CMD pandemic that spread from Uganda in the late 1980s still continues to devastate cassava crops. To assess the association of distinct B. tabaci genetic groups with the CMD pandemic, mitochondrial cytochrome oxidase I gene sequences were analysed from whiteflies collected during surveys conducted from 2010 to 2013 in Tanzania. Four genetic groups – Sub‐Saharan Africa 1 (SSA1), Mediterranean, Indian Ocean and East Africa 1, and a group of unknown whitefly species were identified. SSA1 comprised four subgroups: SSA1‐SG1, SSA1‐SG2, SSA1‐SG1/2 and SSA1‐SG3. SSA1‐SG1 was confined to the pandemic‐affected north‐western parts of Tanzania whilst SSA1‐SG2 and SSA1‐SG3 were found in the central and eastern parts not yet affected by the pandemic. The CMD pandemic front was estimated to lie in Geita Region, north‐western Tanzania, and to be spreading south‐east at a rate of ca 26 km/year. The pandemic‐associated B. tabaci SSA1‐SG1 predominated up to 180 km ahead of the CMD front indicating that changes in whitefly population characteristics precede changes in disease characteristics.     

Stock structure analysis of ‘Bombay duck’ (Harpadon nehereus Hamilton, 1822) along the Indian coast using truss network morphometrics

Harpadon nehereus, commonly known as ‘Bombay duck’, is a fish with a discontinuous distribution along the Indian peninsula. The fisheries are dominant on the north‐east and north‐west coast but are absent in commercial landings below 15° north latitude. Heretofore stock assessment studies had not considered the various spawning stock components that replenish this fishery, therefore the present study. Fish samples were collected from four locations: two each from the northeast and the northwest coasts. Twenty‐four morphometric variables were measured using a box‐truss network method. Factor analysis of these variables differentiated the east and the west coast fish populations. Multiple comparisons on the factor scores indicated two independent stocks on the east coast, whereas the fishery on the west coast is replenished by a single stock. The important morphometric traits that accounted for most of the stock variations were related to swimming adaptations of the fish. Future stock assessments can consider the population on the west coast as a single stock when formulating management plans. To harvest the resource in a sustainable manner, the maritime states on the west coast should adopt collaborative efforts towards managing this fishery.     

EVIDENCE OF A BIOGEOGRAPHIC BREAK BETWEEN POPULATIONS OF A HIGH DISPERSAL STARFISH: CONGRUENT REGIONS WITHIN THE INDO-WEST PACIFIC DEFINED BY COLOR MORPHS,mtDNA, AND ALLOZYME DATA

Both mtDNA variation and allozyme data demonstrate that geographic groupings of different color morphs of the starfish Linckia laevigata are congruent with a genetic discontinuity between the Indian and Pacific Oceans. Populations of L. laevigata sampled from Thailand and South Africa, where an orange color morph predominates, were surveyed using seven polymorphic enzyme loci and restriction fragment analysis of a portion of the mtDNA including the control region. Both allozyme and DNA data demonstrated that these populations were significantly genetically differentiated from each other and to a greater degree from 23 populations throughout the West Pacific Ocean, where a blue color morph is predominant. The genetic structure observed in L. laevigata is consistent with traditional ideas of a biogeographic boundary between the Indian and Pacific Oceans except that populations several hundreds kilometers off the coast of north Western Australia (Indian Ocean) were genetically similar to and had the same color morphs as Pacific populations. It is suggested that gene flow may have continued (possibly at a reduced rate) between these offshore reefs in Western Australia and the West Pacific during Pleistocene falls in sea level, but at the same time gene flow was restricted between these Western Australian populations and those in both Thailand and South Africa, possibly by upwellings. The molecular data in this study suggest that vicariant events have played an important role in shaping the broadscale genetic structure of L. laevigata. Additionally, greater genetic structure was observed among Indian Ocean populations than among Pacific Ocean populations, probably because there are fewer reefs and island archipelagos in the Indian Ocean than in the Pacific, and because present-day surface ocean currents do not facilitate long-distance dispersal.     

Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania

In recent years, a large number of individuals of the species Latimeria chalumnae, one of the living fossil coelacanths, have been landed off the coast of Tanzania. Although L. chalumnae specimens have also been landed at other localities in the western Indian Ocean, so far, viable populations of this species have been identified only at two localities, Comoros and South Africa. Therefore, the recent active catch off Tanzania suggests a new habitat for L. chalumnae. To examine the genetic background of the Tanzanian fish, we analyzed complete mtDNA sequences of two Tanzanian individuals (Kigombe-9 and Songo Mnara-1) collected from the north and south coasts of Tanzania. Using the recently reported criteria for six haplotypes established in a population genetic study for coelacanths living in the western Indian Ocean [Schartl, M., Hornung, U., Hissman, K., Schauer, J., Fricke, H., 2005. Relatedness among east African coelacanths. Nature 435, 901.], we characterized Songo Mnara-1 as haplotype 1 and Kigombe-9 as haplotype 5. We suggest that the Songo Mnara specimen is a member of the Comoran group, but was swept away by the South Equatorial current. The individual from Kigombe may be a member of an undiscovered population that exists near the boundary between Tanzania and Kenya. Further analysis using more than 19 individuals recently captured off the north coast of Tanzania will reveal whether a new population exists there. Our sequence data suggest additional variable sites in the mtDNA sequence that may define the population structure of coelacanths in the western Indian Ocean and also raise the possibility that the previously published Comoran coelacanth mtDNA sequence contains several critical errors including base changes and indels.     

REVIEWS AND RECORDS

Summerhayes, C. P., Hofmeyr. P. K. &; Rioux, R. H. 1974. Seabirds off the southwestern coast of Africa. Ostrich 45: 83–109.

The distribution of seabirds off the southwestern coast of Africa was observed during April. May and November, and observed south of Africa in March. Most seabirds off the west coast were concentrated near to the coast or over the edge of the continental shelf. These are sites where forms of upwelling bring water rich in nutrients to the surface of the sea. The most birds were seen in March, April and May, the least in November. Most common over the shelf-edge were, in order of abundance, Blackbrowed Albatross, Cape Hens, Shy Albatross, Yellownosed Albatross, Wilson's Storm Petrels, Cape Gannets, Common/Arctic Terns, and Antarctic Skuas. Seasonal shifts in their ranges and population densities probably reflect the influence of breeding and migration.

Comparable concentrations of seabirds were only seen as the cold, nutrient-rich waters of the Subantarctic were approached south of Africa. Here turbulence breaks up the front of the Subtropical Convergence and, in moving large masses of cold water northwards, provides a “corridor” which Southern Ocean species may follow to reach Africa.

(Contribution No. 2687 of the Woods Hole Oceanographic Institution).     

Predicting suitable environments and potential occurrences for coelacanths (Latimeria spp.)

Extant coelacanths (Latimeria chalumnae) were first discovered in the western Indian Ocean in 1938; in 1998, a second species of coelacanth, Latimeria menadoensis, was discovered off the north coast of Sulawesi, Indonesia, expanding the known distribution of the genus across the Indian Ocean Basin. This study uses ecological niche modeling techniques to estimate dimensions of realized niches of coelacanths and generate hypotheses for additional sites where they might be found. Coelacanth occurrence information was integrated with environmental and oceanographic data using the Genetic Algorithm for Rule-set Production (GARP) and a maximum entropy algorithm (Maxent). Resulting models were visualized as maps of relative suitability of sites for coelacanths throughout the Indian Ocean, as well as scatterplots of ecological variables. Our findings suggest that the range of coelacanths could extend beyond their presently known distribution and suggests alternative mechanisms for currently observed distributions. Further investigation into these hypotheses could aid in forming a more complete picture of the distributions and populations of members of genus Latimeria, which in turn could aid in developing conservation strategies, particularly in the case of L. menadoensis.     

Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites

Background and Aims

The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.

Methods

Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.

Key Results

Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.

Conclusions

Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.     

Deciphering patterns of transoceanic dispersal: the evolutionary origin and biogeography of coastal lizards (Cryptoblepharus) in the Western Indian Ocean region

Aim Cryptoblepharus is a genus of small arboreal or rock‐dwelling scincid lizards, widespread through the Indo‐Pacific and Australian regions, with a disjunct outlier in the Malagasy region. The taxonomy within this genus is controversial, with different authors ranking the different forms (now some 36) at various levels, from different species to subspecies of a single species, Cryptoblepharus boutonii. We investigated the biogeography and genetic differentiation of the Cryptoblepharus from the Western Indian Ocean region, in order to understand their origin and history. Location Western Indian Ocean region. Methods We analysed sequences of mitochondrial DNA (partial 12s and 16s rRNA genes, 766 bp) from 48 specimens collected in Madagascar, Mauritius, the four Comoros islands and East Africa, and also in New Caledonia, representing the Australo‐Pacific unit of the distribution. Results Pairwise sequence divergences of c. 3.1% were found between the New Caledonian forms and the ones from the Western Indian Ocean. Two clades were identified in Madagascar, probably corresponding to the recognized forms cognatus and voeltzkowi, and two clades were identified in the Comoro islands, where each island population formed a distinct haplotype clade. The East African samples form a monophyletic unit, with some variation existing between Pemba, Zanzibar and continental Tanzania populations. Individuals from Mauritius form a divergent group, more related to populations from Moheli and Grand Comore (Comoros islands) than to the others. Main conclusions The level of divergence between the populations from the Western Indian Ocean and Australian regions and the geographic coherence of the variation within the Western Indian Ocean group are concordant with the hypothesis of a colonization of this region by a natural transoceanic dispersal (from Australia or Indonesia). The group then may have diversified in Madagascar, from where it separately colonized the East African coast, the Comoros islands (twice), and Mauritius. The genetic divergence found is congruent with the known morphological variation, but its degree is much lower than typically seen between distinct species of reptiles.     

Climate‐driven rampant speciation of the Cape flora

Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine‐driven climate change. Location Middle to Late Miocene in the south‐east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south‐east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south‐western African coast are the disappearance of Podocarpus‐dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi‐arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre‐date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine‐driven climate change in south‐western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae.     

Regional movements of satellite‐tagged whale sharks Rhincodon typus in the Gulf of Aden

To gain insight into whale shark (Rhincodon typus) movement patterns in the Western Indian Ocean, we deployed eight pop‐up satellite tags at an aggregation site in the Arta Bay region of the Gulf of Tadjoura, Djibouti in the winter months of 2012, 2016, and 2017. Tags revealed movements ranging from local‐scale around the Djibouti aggregation site, regional movements along the coastline of Somaliland, movements north into the Red Sea, and a large‐scale (>1,000 km) movement to the east coast of Somalia, outside of the Gulf of Aden. Vertical movement data revealed high occupation of the top ten meters of the water column, diel vertical movement patterns, and deep diving behavior. Long‐distance movements recorded both here and in previous studies suggest that connectivity between the whale sharks tagged at the Djibouti aggregation and other documented aggregations in the region are likely within annual timeframes. In addition, wide‐ranging movements through multiple nations, as well as the high use of surface waters recorded, likely exposes whale sharks in this region to several anthropogenic threats, including targeted and bycatch fisheries and ship‐strikes. Area‐based management approaches focusing on seasonal hotspots offer a way forward in the conservation of whale sharks in the Western Indian Ocean.     

New species of Boswellia and Commiphora (Burseraceae) from Somalia

The new species Boswellia globosa, from the foothills of the limestone escarpment along the Gulf of Aden in northern Somalia, and Commiphora lacerata, from a rocky limestone slope near the coast of the Indian Ocean in north‐eastern Somalia, are described and illustrated.     

Habitat and food partitioning of billfishes (Xiphioidei)

Species composition and food habits of four istiophorid billfishes were investigated and compared in three different tropical areas of the eastern North Pacific Ocean by longline operations from September to November 2004. Sailfish Istiophorus platypterus, shortbill spearfish Tetrapturus angustirostris and blue marlin Makaira nigricans had specific habitat preferences and mainly occurred in the near‐continent area (13–16° N; 103–107° W), the open‐ocean area (16–18° N; 118–134° W) and the near‐equator area (5° N; 104–120° W). Small (<140 cm in lower jaw–fork length) striped marlin Kajikia audax mainly occurred in the near‐continent area; however, large (≥140 cm) individuals occurred throughout all three areas. Prey compositions of large K. audax in the three areas were different from one other reflecting the prey availability in each area. In the open‐ocean area, molid fishes were dominant in mass for both large K. audax (49%) and T. angustirostris (73%), and large K. audax also fed on ostraciid (33%) and scombrid fishes (15%). In the near‐continent area, tetraodontid fishes were dominant for large and small I. platypterus (54, 57%), and both large and small K. audax also fed on tetraodontid fishes (3, 12%). Large K. audax in this area fed mainly on scombrid fishes (86%). These results indicate that large K. audax show overlaps but little segregations of its prey with other billfishes. In the near‐equator area, stomach contents of large K. audax and M. nigricans were few and billfish prey items were thought to be scarce.     

Results of satellite tagging of Atlantic bluefin tuna, <Emphasis Type="Italic">Thunnus thynnus</Emphasis>, off the coast of Ireland

Pop-up satellite archival tags were attached to six Atlantic bluefin tuna (Thunnus thynnus) off the west coast of Ireland in autumn 2003 and 2004. The satellite tags measured pressure, ambient temperature and light for the term of deployment. Radio pop-up satellite endpoint positions, light and sea surface temperature estimations of geolocation indicate that two fish tagged minutes apart off the coast of County Donegal, migrated to the eastern and western Atlantic Ocean over the following 8 months. The two fish were 5218 km apart at the termination of the experiment. After tagging in September and popping up the following March and April, one fish had traveled to the western Atlantic while the other was located in the waters off the southwest coast of Portugal. A third fish tagged off the coast of County Donegal in October 2004 moved into the Mediterranean Sea and was caught by a fishing vessel southeast of Malta on 11 June 2005. The results link bluefin tuna feeding on European foraging grounds with known eastern breeding regions and western Atlantic waters.     

Seasonal variation in abundance of the Indian mackerel,Rastrelliger kanagurta Cuvier (Pisces: Scombridae) along the Zanzibar coast of East Africa

Purse-seine catches of the mackerel, Rastrelliger kanagurta Cuvier along the west coast of Zanzibar revealed seasonal patterns of abundance associated with monsoon winds. Low catches were obtained during the south-east monsoons while the north east monsoons were characterised by high catches. The largest sizes of mackerel were caught between June and August with a mixture of large and smaller ones between September and March. Mackerel in spawning condition were common between June and September with immature ones between September and January. The variations in mackerel abundance, size composition, and maturity of the fish are discussed in relation to seasonal changes, fish migrations, recruitment and food supply.     

Phylogeography of the introduced species Rattus rattus in the western Indian Ocean,with special emphasis on the colonization history of Madagascar

Aim To describe the phylogeographic patterns of the black rat, Rattus rattus, from islands in the western Indian Ocean where the species has been introduced (Madagascar and the neighbouring islands of Réunion, Mayotte and Grande Comore), in comparison with the postulated source area (India). Location Western Indian Ocean: India, Arabian Peninsula, East Africa and the islands of Madagascar, Réunion, Grande Comore and Mayotte. Methods Mitochondrial DNA (cytochrome b, tRNA and D‐loop, 1762 bp) was sequenced for 71 individuals from 11 countries in the western Indian Ocean. A partial D‐loop (419 bp) was also sequenced for eight populations from Madagascar (97 individuals), which were analysed in addition to six previously published populations from southern Madagascar. Results Haplotypes from India and the Arabian Peninsula occupied a basal position in the phylogenetic tree, whereas those from islands were distributed in different monophyletic clusters: Madagascar grouped with Mayotte, while Réunion and Grand Comore were present in two other separate groups. The only exception was one individual from Madagascar (out of 190) carrying a haplotype that clustered with those from Réunion and South Africa. ‘Isolation with migration’ simulations favoured a model with no recurrent migration between Oman and Madagascar. Mismatch distribution analyses dated the expansion of Malagasy populations on a time‐scale compatible with human colonization history. Higher haplotype diversity and older expansion times were found on the east coast of Madagascar compared with the central highlands. Main conclusions Phylogeographic patterns supported the hypothesis of human‐mediated colonization of R. rattus from source populations in either the native area (India) or anciently colonized regions (the Arabian Peninsula) to islands of the western Indian Ocean. Despite their proximity, each island has a distinct colonization history. Independent colonization events may have occurred simultaneously in Madagascar and Grande Comore, whereas Mayotte would have been colonized from Madagascar. Réunion was colonized independently, presumably from Europe. Malagasy populations may have originated from a single successful colonization event, followed by rapid expansion, first in coastal zones and then in the central highlands. The congruence of the observed phylogeographic pattern with human colonization events and pathways supports the potential relevance of the black rat in tracing human history.     

Migratory routes of red‐necked phalaropes Phalaropus lobatus breeding in southern Chukotka revealed by geolocators

The migration routes of red‐necked phalaropes breeding around the Bering Sea are poorly known, despite the fact that the Bering Sea could mark the boundary between the East Palearctic populations that winter in the Pacific Ocean around the East Indies and the West Nearctic populations that winter in the Pacific Ocean off the coast of South America. Geolocator data retrieved from two male phalaropes tagged in southern Chukotka, Far Eastern Russia, confirm that birds breeding in this region belong to the East Palearctic population and winter in the East Indies, suggesting that the division line with the West Nearctic population is farther to the east. The routes taken by the two phalaropes were almost entirely pelagic, totaling around 18 000–20 000 km round‐trip, with the birds continuously on the move during migration, rather than resident in any particular stopover site, contrary to most other migratory shorebirds.