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.     

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.     

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.     

The evolution of the Indian Ocean parrots (Psittaciformes): extinction, adaptive radiation and eustacy

Parrots are among the most recognisable and widely distributed of all bird groups occupying major parts of the tropics. The evolution of the genera that are found in and around the Indian Ocean region is particularly interesting as they show a high degree of heterogeneity in distribution and levels of speciation. Here we present a molecular phylogenetic analysis of Indian Ocean parrots, identifying the possible geological and geographical factors that influenced their evolution. We hypothesise that the Indian Ocean islands acted as stepping stones in the radiation of the Old-World parrots, and that sea-level changes may have been an important determinant of current distributions and differences in speciation. A multi-locus phylogeny showing the evolutionary relationships among genera highlights the interesting position of the monotypic Psittrichas, which shares a common ancestor with the geographically distant Coracopsis. An extensive species-level molecular phylogeny indicates a complex pattern of radiation including evidence for colonisation of Africa, Asia and the Indian Ocean islands from Australasia via multiple routes, and of island populations ‘seeding’ continents. Moreover, comparison of estimated divergence dates and sea-level changes points to the latter as a factor in parrot speciation. This is the first study to include the extinct parrot taxa, Mascarinus mascarinus and Psittacula wardi which, respectively, appear closely related to Coracopsis nigra and Psittacula eupatria.     

Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys)

The origin of the terrestrial biota of Madagascar and, especially, the smaller island chains of the western Indian Ocean is relatively poorly understood. Madagascar represents a mixture of Gondwanan vicariant lineages and more recent colonizers arriving via Cenozoic dispersal, mostly from Africa. Dispersal must explain the biota of the smaller islands such as the Comoros and the chain of Mascarene islands, but relatively few studies have pinpointed the source of colonizers, which may include mainland Africa, Asia, Australasia, and Madagascar. The pantropical hermit spiders (genus Nephilengys) seem to have colonized the Indian Ocean island arc stretching from Comoros through Madagascar and onto Mascarenes, and thus offer one opportunity to reveal biogeographical patterns in the Indian Ocean. We test alternative hypotheses on the colonization route of Nephilengys spiders in the Indian Ocean and simultaneously test the current taxonomical hypothesis using genetic and morphological data. We used mitochondrial (COI) and nuclear (ITS2) markers to examine Nephilengys phylogenetic structure with samples from Africa, southeast Asia, and the Indian Ocean islands of Madagascar, Mayotte, Réunion and Mauritius. We used Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, and calculated genetic distances and fixation indices. Our results suggest an African origin of Madagascar Nephilengys via Cenozoic dispersal, and subsequent colonization of the Mascarene islands from Madagascar. We find strong evidence of gene flow across Madagascar and through the neighboring islands north of it, while phylogenetic trees, haplotype networks, and fixation indices all reveal genetically isolated and divergent lineages on Mauritius and Réunion, consistent with female color morphs. These results, and the discovery of the first males from Réunion and Mauritius, in turn falsify the existing taxonomic hypothesis of a single widespread species, Nephilengys borbonica, throughout the archipelago. Instead, we diagnose three Nephilengys species: Nephilengys livida (Vinson, 1863) from Madagascar and Comoros, N. borbonica (Vinson, 1863) from Réunion, and Nephilengys dodo new species from Mauritius. Nephilengys followed a colonization route to Madagascar from Africa, and on through to the Mascarenes, where it speciated on isolated islands. The related golden orb-weaving spiders, genus Nephila, have followed the same colonization route, but Nephila shows shallower divergencies, implying recent colonization, or a moderate level of gene flow across the archipelago preventing speciation. Unlike their synanthropic congeners, N. borbonica and N. dodo are confined to pristine island forests and their discovery calls for evaluation of their conservation status.     

Cross-Mating Compatibility and Competitiveness among Aedes albopictus Strains from Distinct Geographic Origins - Implications for Future Application of SIT Programs in the South West Indian Ocean Islands

The production of large numbers of males needed for a sustainable sterile insect technique (SIT) control program requires significant developmental and operational costs. This may constitute a significant economic barrier to the installation of large scale rearing facilities in countries that are undergoing a transition from being largely dependent on insecticide use to be in a position to integrate the SIT against Aedes albopictus. Alternative options available for those countries could be to rely on outsourcing of sterile males from a foreign supplier, or for one centralised facility to produce mosquitoes for several countries, thus increasing the efficiency of the mass-rearing effort. However, demonstration of strain compatibility is a prerequisite for the export of mosquitoes for transborder SIT applications. Here, we compared mating compatibility among Ae. albopictus populations originating from three islands of the South Western Indian Ocean, and assessed both insemination rates and egg fertility in all possible cross-mating combinations. Furthermore, competitiveness between irradiated and non-irradiated males from the three studied strains, and the subsequent effect on female fertility were also examined. Although morphometric analysis of wing shapes suggested phenoptypic differences between Ae. albopictus strains, perfect reproductive compatibility between them was observed. Furthermore, irradiated males from the different islands demonstrated similar levels of competitiveness and induced sterility when confronted with fertile males from any of the other island populations tested. In conclusion, despite the evidence of inter-strain differences based on male wing morphology, collectively, our results provide a new set of expectations for the use of a single candidate strain of mass-reared sterile males for area-wide scale application of SIT against Ae. albopictus populations in different islands across the South Western Indian Ocean. Cross-mating competitiveness tests such as those applied here are necessary to assess the quality of mass reared strains for the trans-border application of sterile male release programs.     

Haemoproteus iwa in Great Frigatebirds (Fregata minor) in the Islands of the Western Indian Ocean

Blood parasites of the sub-genus Haemoproteus have been reported in seabirds, in particular in species in the Suliformes order. These parasites are transmitted by hippoboscid flies of the genus Olfersia; strong specificity has been suggested between the vector and its vertebrate host. We investigated the prevalence of Haemoproteus infection in Suliformes and hippoboscid flies in two oceanic islands of the Western Indian Ocean: Europa and Tromelin. In total, 209 blood samples were collected from great frigatebirds (Fregata minor), masked boobies (Sula dactylatra) and red-footed boobies (Sula sula). Forty-one hippoboscid flies were also collected from birds. Seventeen frigatebirds and one fly collected on Europa tested positive for the presence of Haemoproteus parasites by polymerase chain reaction. Phylogenetic analyses based on partial sequences of the Cytochrome b gene showed that parasites were closely related to Haemoproteus iwa reported from frigatebirds in the Pacific Ocean and in the Caribbean. Plasmodium was also detected in a frigatebird on Europa; however, its placement on the phylogenetic tree could not be resolved. We provide strong support for transmission of blood parasites in seabirds in the Western Indian Ocean and suggest that migrations between the Pacific and the Indian oceans could favor the large-scale distribution of Haemoproteus iwa in frigatebird populations.     

Genetic differentiation in the mud crab Scylla serrata (Decapoda: Portunidae) within the Indian Ocean

Scylla serrata (Decapoda: Portunidae) is a swimming crab that is widespread in the Indo-Pacific region and commonly found in estuarine and mangrove waters. An extended planktonic larval phase suggests high dispersal potential and the possibility of extensive gene flow between conspecific populations at least on a geographic mesoscale (tens to hundreds of kilometres).Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 77 individuals from four representative mangrove swamps of the African tropics (Kenya and Zanzibar) by means of DNA sequencing. We examined 535 base pairs (bp) and identified 24 different haplotypes. Each population sample is characterised by a single most frequent haplotype, shared among all four populations, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population.Analysis of molecular variance (AMOVA), F_ST statistics and χ² contingency analysis of spatial distribution of mtDNA haplotype frequencies revealed in toto a significant genetic differentiation among populations. These results could indicate that gene flow might be reduced, even between geographically close sites, despite the high potential for dispersal; anyway, at the recorded level of divergence and owing to the abundance of rare haplotypes and singletons in our data set, repeated sampling over time is necessary to establish whether the recorded pattern of genetic differentiation is stable and biologically significant.Finally, integration of our data with those reported by Gopurenko et al. [Mar. Biol. 134 (1999) 227] on S. serrata from South Africa, Red Sea and Mauritius Islands allowed to infer S. serrata population structure within a larger area of the Indian Ocean region.     

The origin of Rattus rattus on the Îles Éparses,Western Indian Ocean

Tollenaere et al. (Journal of Biogeography, 2010, 37 , 398–410) present a phylogeographic analysis of Rattus rattus for the Western Indian Ocean, with particular emphasis on Madagascar, but do not include samples from three island groups centrally located in the Mozambique Channel. Haplotypes from these islands provide additional information on the colonization pathways of R. rattus in the Western Indian Ocean region. For each of the three Îles Éparses groups in the Mozambique Channel, we test the competing hypotheses that colonization by R. rattus was most likely: (1) from the Arabian Peninsula, (2) from East Africa, (3) from Madagascar, or (4) from independent shipping. These results are combined with historical observations of the presence of R. rattus on these islands to give stronger inference on the colonization pathways. Additionally, more accurate colonization dates provide guidance for contemporary conservation management.     

Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae)

We constructed a phylogenetic hypothesis for western Indian Ocean sunbirds (Nectarinia) and used this to investigate the geographic pattern of their diversification among the islands of the Indian Ocean. A total of 1309 bp of mitochondrial sequence data was collected from the island sunbird taxa of the western Indian Ocean region, combined with sequence data from a selection of continental (African and Asian) sunbirds. Topological and branch length information combined with estimated divergence times are used to present hypotheses for the direction and sequence of colonization events in relation to the geological history of the Indian Ocean region. Indian Ocean sunbirds fall into two well-supported clades, consistent with two independent colonizations from Africa within the last 3.9 million years. The first clade contains island populations representing the species Nectarinia notata, while the second includes Nectarinia souimanga, Nectarinia humbloti, Nectarinia dussumieri, and Nectarinia coquereli. With respect to the latter clade, application of Bremer's [Syst. Biol. 41 (1992) 436] ancestral areas method permits us to posit the Comoros archipelago as the point of initial colonization in the Indian Ocean. The subsequent expansion of the souimanga clade across its Indian Ocean range occurred rapidly, with descendants of this early expansion remaining on the Comoros and granitic Seychelles. The data suggest that a more recent expansion from Anjouan in the Comoros group led to the colonization of Madagascar by sunbirds representing the souimanga clade. In concordance with the very young geological age of the Aldabra group, the sunbirds of this archipelago have diverged little from the Madagascar population; this is attributed to colonization of the Aldabra archipelago in recent times, in one or possibly two or more waves originating from Madagascar. The overall pattern of sunbird radiation across Indian Ocean islands indicates that these birds disperse across ocean barriers with relative ease, but that their subsequent evolutionary success probably depends on a variety of factors including prior island occupation by competing species.     

Metagenomic Exploration of Viruses throughout the Indian Ocean

The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction (<0.1 µm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions.     

Comparative phylogeography of the western Indian Ocean reef fauna

Assessing patterns of connectivity at the community and population levels is relevant to marine resource management and conservation. The present study reviews this issue with a focus on the western Indian Ocean (WIO) biogeographic province. This part of the Indian Ocean holds more species than expected from current models of global reef fish species richness. In this study, checklists of reef fish species were examined to determine levels of endemism in each of 10 biogeographic provinces of the Indian Ocean. Results showed that the number of endemic species was higher in the WIO than in any other region of the Indian Ocean. Endemic species from the WIO on the average had a larger body size than elsewhere in the tropical Indian Ocean. This suggests an effect of peripheral speciation, as previously documented in the Hawaiian reef fish fauna, relative to other sites in the tropical western Pacific. To explore evolutionary dynamics of species across biogeographic provinces and infer mechanisms of speciation, we present and compare the results of phylogeographic surveys based on compilations of published and unpublished mitochondrial DNA sequences for 19 Indo-Pacific reef-associated fishes (rainbow grouper Cephalopholis argus, scrawled butterflyfish Chaetodon meyeri, bluespot mullet Crenimugil sp. A, humbug damselfish Dascyllus abudafur/Dascyllus aruanus, areolate grouper Epinephelus areolatus, blacktip grouper Epinephelus fasciatus, honeycomb grouper Epinephelus merra, bluespotted cornetfish Fistularia commersonii, cleaner wrasse Labroides sp. 1, longface emperor Lethrinus sp. A, bluestripe snapper Lutjanus kasmira, unicornfishes Naso brevirosris, Naso unicornis and Naso vlamingii, blue-spotted maskray Neotrygon kuhlii, largescale mullet Planiliza macrolepis, common parrotfish Scarus psicattus, crescent grunter Terapon jarbua, whitetip reef shark Triaenodon obesus) and three coastal Indo-West Pacific invertebrates (blue seastar Linckia laevigata, spiny lobster Panulirus homarus, small giant clam Tridacna maxima). Heterogeneous and often unbalanced sampling design, paucity of data in a number of cases, and among-species discrepancy in phylogeographic structure precluded any generalization regarding phylogeographic patterns. Nevertheless, the WIO might have been a source of haplotypes in some cases and it also harboured an endemic clade in at least one case. The present survey also highlighted likely cryptic species. This may eventually affect the accuracy of the current checklists of species, which form the basis of some of the recent advances in Indo-West Pacific marine ecology and biogeography.     

Reproductive compatibility and genetic and morphometric variability among populations of the predatory mite,Amblyseius largoensis (Acari: Phytoseiidae), from Indian Ocean Islands and the Americas

The red palm mite (RPM), Raoiella indica Hirst (Acari: Tenuipalpidae), is an invasive phytophagous mite that was recently introduced into The Americas. The predatory mite Amblyseius largoensis Muma (Acari: Phytoseiidae) has been the only natural enemy consistently found in association with RPM. This study aimed to determine if A. largoensis populations from the Indian Ocean Islands (La Réunion and Mauritius) and the Americas (Brazil, Trinidad and Tobago and the USA) consist a taxonomic unit or a group of cryptic species. First, the morphological variability among the A. largoensis populations from these areas was evaluated through morphometric analyses of 36 morphological traits. Then, their genetic variability and phylogenetic relationships were assessed based on two target DNA fragments: the nuclear Internal Transcribed Spacer and the mithochondrial 12S rRNA. Finally, reproductive compatibility of the populations from La Réunion and Roraima, Brazil was evaluated. Morphometric differences between the A. largoensis specimens from La Réunion Island and the Americas were observed, most of them on the length of the setae. Molecular analysis indicated that the A. largoensis populations from the Indian Ocean Islands and the Americas belong to the same taxonomic entity, although to two well defined genetic groups. Crossings involving the A. largoensis populations from La Réunion Island and Roraima, Brazil revealed complete reproductive compatibility between these populations. Information on the morphometric and genetic variability among studied A. largoensis populations can be further exploited in future studies to follow colonization of Indian Ocean Islands populations in the Americas, in the case of field releases.     

Geographical gradients in the genome size variation of wild coffee trees (Coffea) native to Africa and Indian Ocean islands

The genus Coffea, mainly native to Africa and to the Indian Ocean islands (Mascarocoffea), accounts for 124 species. Genome size data are available for 23 African species. The aim of this study was to assess the genome size of 44 Mascarocoffea species and to investigate possible association with species geographic distribution, stomata traits, and species relationships. 2?C values were measured using flow cytometry. A lyophilization procedure for leaves was tested. The 2?C nuclear DNA content of Mascarocoffea species ranged from 0.96 to 1.41?pg. Coffea mauritiana and Coffea humblotiana have the smallest genomes and Coffea millotii has the largest. Mean 2?C DNA for Mascarocoffea and Africa is 1.19 and 1.43?pg, respectively. The overall DNA values corresponded to two partially overlapped normal distributions: one harboring species from east Africa Mascarocoffea, the other harboring species from west/central Africa. Plotted on a geographical map according to the native origin of species, these values showed a gradient in Madagascar and Africa. Genome sizes increased following a north to southeast gradient in Madagascar and an east to west gradient in Africa. None, or only weak correlations were noted between genome size and stomata parameters. Genetically close species could be highly distinctive in their genome size while divergent species could be similarly sized. The non-random geographic distribution and habitat of species, and the absence of correlation between genome size and genetic relationships, suggest that during Coffea genome evolution, both DNA content increase and/or decrease occurred independently in Africa and in the Indian Ocean Islands.     

Worldwide Distribution of the MYH9 Kidney Disease Susceptibility Alleles and Haplotypes: Evidence of Historical Selection in Africa

MYH9 was recently identified as renal susceptibility gene (OR 3–8, p<10⁻⁸) for major forms of kidney disease disproportionately affecting individuals of African descent. The risk haplotype (E-1) occurs at much higher frequencies in African Americans (≥60%) than in European Americans (<4%), revealing a genetic basis for a major health disparity. The population distributions of MYH9 risk alleles and the E-1 risk haplotype and the demographic and selective forces acting on the MYH9 region are not well explored. We reconstructed MYH9 haplotypes from 4 tagging single nucleotide polymorphisms (SNPs) spanning introns 12–23 using available data from HapMap Phase II, and by genotyping 938 DNAs from the Human Genome Diversity Panel (HGDP). The E-1 risk haplotype followed a cline, being most frequent within sub-Saharan African populations (range 50–80%), less frequent in populations from the Middle East (9–27%) and Europe (0–9%), and rare or absent in Asia, the Americas, and Oceania. The fixation indexes (F_ST) for pairwise comparisons between the risk haplotypes for continental populations were calculated for MYH9 haplotypes; F_ST ranged from 0.27–0.40 for Africa compared to other continental populations, possibly due to selection. Uniquely in Africa, the Yoruba population showed high frequency extended haplotype length around the core risk allele (C) compared to the alternative allele (T) at the same locus (rs4821481, iHs = 2.67), as well as high population differentiation (F_{ST(CEU vs. YRI)} = 0.51) in HapMap Phase II data, also observable only in the Yoruba population from HGDP (F_ST = 0.49), pointing to an instance of recent selection in the genomic region. The population-specific divergence in MYH9 risk allele frequencies among the world''s populations may prove important in risk assessment and public health policies to mitigate the burden of kidney disease in vulnerable populations.     

Genetic diversity, geographical range and origin of Bemisia tabaci (Hemiptera: Aleyrodidae) Indian Ocean Ms

The whitefly Bemisia tabaci is a pest vector of begomoviruses on crops worldwide. Bemisia tabaci is composed of a complex of cryptic species which barely interbreed. An exception is the Ms from the South West Indian Ocean (SWIO), which crosses in low proportions with the exotic B. The Ms, together with B and Q is part of the same phylogenetic clad. To infer the genetic structure, the geographical range and putative origin of this putative species, microsatellite data and mitochondrial DNA (cytochrome oxydase I) sequences were analysed on an extensive sample set, including all the islands of the region and samples from mainland Africa. Only B and Ms populations were detected across these islands. The exotic B was found only on the islands of Réunion and Mauritius, whereas the Ms is found on all the SWIO islands. Very high isolation by distance was found for the Ms populations between islands of the SWIO, suggesting a long period of presence in this region. Ms populations from mainland Africa had a higher COI diversity than the Ms of the SWIO islands. This diversity is correlated with size and geological ages of the SWIO islands. The population genetic data obtained are in accordance with an origin of Ms in Africa, followed by its expansion and evolution across the SWIO islands prior to human arrival, confirming the status of Ms as indigenous in the SWIO islands.     

Movement and habitat use of striped marlin Kajikia audax in the Western Indian Ocean

Striped marlin Kajikia audax are globally Near Threatened and their stock in the Indian Ocean was last assessed as “overfished and subject to overfishing”. Significant gaps in our understanding of their ecology remain, hampering the efforts of fisheries managers to ensure stock sustainability. There is a particular lack of fisheries-independent data. Here we present the results from the first large-scale satellite tracking study of K. audax in the Indian Ocean. We tagged 49 K. audax with pop-up archival satellite-linked tags off the Kenyan coast from 2015 to 2019. Individuals were highly mobile, covering horizontal distances of up to 9187 km over periods ranging up to 183 days, with a mean daily distance of ~48 km. Long-distance movements were recorded to the east and north of East Africa, with the most distant tracks extending north to the Arabian Sea and east to near the Maldives. None of the K. audax swam south of East Africa. Kernel utilization distributions of fish locations demonstrated their shifting seasonal activity hotspots. Over the sport-fishing season (and tagging period) in Kenya, from December to March, K. audax typically stayed off the East African coast. After March, the activity hotspot shifted north to a region close to the Horn of Africa and Socotra Island. Remotely sensed sea surface temperature and chlorophyll-a maps indicated that this seasonal movement could be driven by a shift in prey availability. Our results show the high mobility of K. audax in the Western Indian Ocean, and that individuals seasonally range between two major fishing areas.     

The evolutionary origin of Indian Ocean tortoises (Dipsochelys)

Today, the only surviving wild population of giant tortoises in the Indian Ocean occurs on the island of Aldabra. However, giant tortoises once inhabited islands throughout the western Indian Ocean. Madagascar, Africa, and India have all been suggested as possible sources of colonization for these islands. To address the origin of Indian Ocean tortoises (Dipsochelys, formerly Geochelone gigantea), we sequenced the 12S, 16S, and cyt b genes of the mitochondrial DNA. Our phylogenetic analysis shows Dipsochelys to be embedded within the Malagasy lineage, providing evidence that Indian Ocean giant tortoises are derived from a common Malagasy ancestor. This result points to Madagascar as the source of colonization for western Indian Ocean islands by giant tortoises. Tortoises are known to survive long oceanic voyages by floating with ocean currents, and thus, currents flowing northward towards the Aldabra archipelago from the east coast of Madagascar would have provided means for the colonization of western Indian Ocean islands. Additionally, we found an accelerated rate of sequence evolution in the two Malagasy Pyxis species examined. This finding supports previous theories that shorter generation time and smaller body size are related to an increase in mitochondrial DNA substitution rate in vertebrates.     

Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups

Background

Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected.

Methodology/Principal Findings

To elucidate the genetic diversity of Schistosoma haematobium, a DNA ‘barcoding’ study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands.

Conclusions/Significance

The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic ‘bottleneck’ followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis.     

Gene flow and genetic structure of Sicyopterus lagocephalus in the south-western Indian Ocean, assessed by intron-length polymorphism

Sicyopterus lagocephalus is the most abundant sicydiine (amphidromous gobiid) in the rivers of volcanic islands in the south-western Indian Ocean. The species occurs in the Mascarene (Mauritius and La Réunion) and Comoros islands (Anjouan, Mayotte, etc.) and the post-larvae supply an economically important fishery. Because of the scarcity of available ecological and biological data, a genetic survey has been undertaken at the scale of the south-western Indian Ocean using intron-length polymorphism. Samples from La Réunion, Mauritius and Mayotte were used to assess the population genetic structure within islands and between nearby and remote islands. No genetic divergences were observed in samples at these different geographical scales. A lower number of rare alleles were observed in Mayotte samples suggesting a slight effect of their peripheral geographical position. However, no recent bottleneck was evidenced for these populations. High temporal divergences have been demonstrated in La Réunion as in previous studies indicating a temporal Wahlund effect. In the light of these results, the dispersion abilities, the connectivity of populations and the metapopulation functioning are discussed in relation to the regional environmental factors (dispersal barriers, habitat colonization, cyclones, long distance dispersal).