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Insect pest invasions pose a major threat to agriculture, forestry and many natural ecosystems. Thaumastocoris peregrinus is an invasive sap-sucking pest of significant economic importance to Eucalyptus forestry that has recently invaded several countries worldwide. In this study we identify the origin and retrace the invasion history of T. peregrinus. We analysed samples from six locations in Africa, South America and Australia using microsatellites markers and a combination of clustering methods and scenario testing using Approximate Bayesian Clustering. We detected clear genetic substructure differentiating African and South American samples, with representatives of both present in Australia. The Australian population from New South Wales showed substantially higher genetic diversity than the Queensland source, which could indicate that this region could be part of the core range and evolutionary origin of the species. Africa and South America were colonised by independent introductions that occurred more or less concurrently. The study illustrates the impact of the bridgehead effect on global invasions following an outbreak or ‘invasion’ within a city in the native range of the insect.

We describe novel hybrid primers for the successful amplification and sequencing of the mitochondrial cytochrome b (cytb) gene in the family Siganidae. We aligned 403 cytb sequences from 29 species and found multiple potential conserved hybrid primers (

International audience; A continuing impediment to the taxonomy of the reticulate whipray Himantura spp. species complex is the absence of a type specimen for H. uarnak (Gmelin [ex Forsskål], 1789). Here, reticulate whipray specimens were sampled from the Jeddah region in the Red Sea, the assumed type locality of H. uarnak, and characterized genetically at the cytochrome-oxidase subunit 1 (CO1) locus. One of these specimens now in the fish collection of the California Academy of Sciences was designated as neotype. The maximum-likelihood phylogeny of all available CO1 gene sequences from the genus Himantura had the following topology: ((H. leoparda, H. uarnak), (H. undulata, (Himantura sp. 2, (H. australis + Himantura sp. 1))), H. tutul), where H. uarnak haplotypes formed a distinct lineage sister to H. leoparda. Based on these CO1 gene sequences, the geographic distribution of H. uarnak includes the eastern Mediterranean, the Red Sea, the East African coast, and the Arabian Sea. At least one lineage in the reticulate whipray species complex remains to be named.

The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.

Members of the Tree Protection Co-operative Programme (TPCP), the THRIP Initiative of the Department of Trade and Industry and the National Research Foundation (NRF) (NRF Grant Number 88227).

International audience; AimTo investigate whether the populations of 17 widespread hydroid species are connected on a demographic level (one to few generations) or are mostly connected on evolutionary timescales.LocationCoral reefs of the South‐western Indian Ocean.Taxon17 widespread hydroid species (Cnidaria, Hydrozoa).MethodsUsing mitochondrial (16S) and nuclear (Calmodulin) sequences, we analysed 17 co‐distributed hydroid species with contrasting life history traits (with or without a pelagic life history phase). We used DNA‐based species delimitation methods, haplotype networks, analysis of molecular variance, and Bayesian skyline plots to investigate diversification and connectivity patterns in the region.ResultsPutative cryptic species were revealed in half of the species and the 17 species resulted in 54 cryptic lineages. The high isolation of hydroid populations in the region is underlined by the rarity of shared haplotypes among localities in most of the species studied. In contrast, haplotypes shared between specimens collected in different ocean basins were found in three species and suggest recent introductions via human activities. The presence of a short pelagic dispersal phase did not seem to increase the connectivity levels of the studied populations, as no significant differences in genetic structure were detected between species with contrasting life history traits.Main conclusionsThese results highlight once again our incomplete knowledge of the marine invertebrate fauna, as we might be underestimating hydroid diversity by two‐thirds, and are discussed in terms of diversification processes, dynamics of the Indo‐Pacific biodiversity and the role of its peripheral marine provinces.

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep-water hake Merluccius paradoxus and the shallow-water hake Merluccius capensis. A total of 14 microsatellites were polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (FST < 0·006) that will be valuable to delimit and characterize genetic stocks.

International audience; Due to their geographic isolation, biotas of oceanic islands are likely influenced by episodic long distance dispersal events, but such observations are scarce. In June 2012, fishermen from Réunion Island caught an unknown specimen of grouper, identified as dusky grouper Epinephelus marginatus (Lowe, 1834). This was highly unexpected considering the large distance of its closest verified occurrence (South Africa, ∼2500 km). To identify the origin of this specimen and the mechanisms driving this potential long distance colonization, we combined genetic analyses and hydrodynamic connectivity modeling approaches. Molecular markers and samples from various locations across the distribution range resulted in the identification of three putative source populations. The Réunion specimen clustered genetically with South Africa. The estimated spawning period in relation to the connectivity modeling of larvae showed no possible direct connection between South Africa and Réunion. However, connectivity was predicted through intermediate stepping stone populations likely located around the southern tip of Madagascar, where the occurrence of the species has yet to be verified. The results further highlight the potential role of the cyclone Bingiza (February 2011) in the connection between Madagascar and Réunion. This shows that cyclones may be an important driver in long distance colonization of oceanic islands.

Appropriate management of invasive fungi requires adequate understanding of their global diversities and movement histories. The fungus Leptographium procerum is associated with root-colonizing forest insects in pine forests throughout the world, and may have contributed to the aggressive behaviour of the red turpentine beetle (Dendroctonus valens) in the beetle's invasive range in China. We used microsatellites and mating type loci to investigate the global diversity of L. procerum and the source population of L. procerum associated with D. valens in China. Clustering analyses supported the separation of the fungal data set into three genetically and geographically-distinct clusters: Europe, North America, and China. The fungus had the highest genetic diversity in Europe, followed by North America and China. Analyses using Approximate Bayesian Computation supported Europe as the most likely source of the North American and Chinese populations. Overall, the results suggested that Europe is the global centre of diversity of L. procerum. Furthermore, they suggested that L. procerum most likely arrived in China independently of D. valens and adopted this beetle as a vector after its introduction.

Compared to endemics, widespread species are of particular interest to retrace recent evolutionary history. These species have a large population size which provides a clearer genetic signature of past events. Moreover, their wide geographic range increases the potential occurrence of evolutionary events (expansion, divergence, etc.). Here, we used several coalescent-based methods to disentangle the evolutionary history of a widespread amphidromous goby (Sicyopterus lagocephalus), in the light of sea-level variations during the Pleistocene. Using 75 samples recovered from three biogeographic regions (Western Indian Ocean, Melanesia and Polynesia), we analysed a portion of the cytochrome b gene and confirmed three major haplogroups, each specific to a region. Furthermore, we found that: (1) the Melanesian haplogroup was the oldest while the two peripheral regions hosted daughter haplogroups; (2) two centrifugal colonisation events occurred from Melanesia to the periphery, each synchronised with periods of strong paleo-ENSO episodes; (3) the demographic contraction–expansion events were linked to Pleistocene sea-level changes; (4) Melanesia and Polynesia acted as efficient refuges during the Last Glacial Maximum. These results highlight the importance of studying widespread species to better understand the role of climate changes and paleo-oceanography on the evolution of biodiversity.

Habitat fragmentation is a major force that will influence the evolution of a species and its distribution range. Pomatoschistus minutus, the sand goby, has a North Atlantic–Mediterranean distribution and shows various level of habitat fragmentation along its geographic repartition. The use of mitochondrial sequences of the cytochrome b (cyt b) gene and two co-dominant sets of nuclear markers (introns and microsatellites) allowed us to describe the relationships between P. minutus populations belonging to several different geographical regions of Europe and to assess the structure of populations inhabiting the Golfe du Lion, along the French Mediterranean coast. The present study confirms that the taxon located in the Adriatic Sea (Venice) should be considered as a distinct species, separated approximately 1.75 Mya. The comparison of P. minutus between the Atlantic and western Mediterranean coasts using polymorphic co-dominant markers revealed that they belong to two demographically independent units, and thus could be considered as well as distinct species, more recently separated (0.3 Mya). The Pleistocene glaciations seem therefore to have played an important role in the diversification of this complex. Finally, at a regional scale in the Golfe du Lion, P. minutus appears to form a single huge homogeneous population. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 175–198.

Within the brittle star genus Amphipholis, individuals are generally small, gonochoric, broadcast spawners, and species often have restricted distribution areas. In contrast, A. squamata (Ophiuroidea, Echinodermata)—a species complex found worldwide—is hermaphroditic and broods its young. We used 2 complementary methods to estimate the selfing rates of this species in the north- western Mediterranean Sea. First, we analysed 190 specimens from Les Goudes (France) using 3 co- dominant microsatellites and deduced the selfing rates from heterozygote deficiency, developing an original method to infer confidence intervals. Not a single heterozygote was discovered, leading to estimated selfing rates of 1.0 for all species, with an inferior limit between 0.77 and 0.98. In 7 other European localities, not a single heterozygote was found. Second, we analysed 91 brooders and their 369 offspring using 7 nuclear markers. All progeny had DNA fingerprints identical to those of the par- ents, confirming that selfing rates are very high. Such high selfing rates, by contributing to coloniza- tion success (Baker's rule), may solve the paradox of cosmopolitism for these ophiuroids that lack a larval phase that would, in theory, ensure dispersal.

Cotylopus rubripinnis, new species, is described on the basis of nine specimens collected from the Island of Mayotte (Comoros), Indian Ocean. Cotylopus rubripinnis differs from the only other known species in the genus (C. acutipinnis Guichenot, 1863) in usually having fewer scales in lateral (LS), transverse back (TRB), transverse forward (TRF), and zigzag series (ZZ), and in having pectoral, dorsal and caudal fins reddish. The genus was previously only known from the Mascarene Islands (Reunion and Mauritius). The discovery of a second species for that rare and endemic genus 1400 km farther to the north‐west in the Indian Ocean is discussed.

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.

The taxonomy of the genus Ophiocoma was last revised by Devaney in 1970. Recent discoveries of new species and re-instatement of previously synonymized names suggest that we still do not fully understand the species limits in this genus. A recent biodiversity survey of the SW Indian Ocean shallow reefs strongly suggested an unrecognised species in the genus, closely related to O. brevipes/O. dentata. This study examined both the molecular phylogenetic relationships and the morphological characteristics of several species in the genus in order to characterise the unrecognised species. The focal species clusters with O. brevipes, O. dentata, O. doederleini within a monophyletic clade supported by molecular data for the first time. The name Breviturma subgen. nov. is proposed for this clade, previously known as brevipes group. Type material of nominal species that have been synonymized with O. dentata was examined and re-assessed. Ophiocoma marmorata proved not conspecific with O. dentata. A rarely used character, dorsal disc granule density, was tested and showed differences between the examined species at similar sizes. In combination with colour pattern, disc granule density, arm spine sequence and maximum disc size, the new species was delimited morphologically and described as Ophiocoma krohi sp. nov.

Aim The global biodiversity crisis requires the identification of regions with high evolutionary potential, i.e. evolutionary hotspots (evospots). We created an analytical framework based on comparative phylogeography and coalescent methods to assess the dynamics of diversification and population persistence in the reef ecosystem of a little-studied region: the Southwestern Indian Ocean (SWIO). Location Coral reefs of the SWIO, with comparative data from the Pacific Ocean. Methods We generated sequences of mitochondrial DNA (COI and 16S) for 10 widespread brittle-stars (345 specimens) from 21 localities (8 in the SWIO). We analysed them by combining comparative phylogeography approaches, coalescent-based methods, molecular clocks and the concept of evolutionarily significant units (ESUs) to draw conclusions about the drivers of biodiversity in the region. Results Cryptic diversity was prevalent, increasing lineage diversity within the 10 nominal species by 70% within the SWIO and by 200% across the Indo-West Pacific. All seven new SWIO lineages meet the criteria for ESUs and at least six are biological species. We detected likely intraregional diversifications dating to the Plio-Pleistocene, supporting the SWIO as a generator of biodiversity. Geographical restriction of ESUs, long coalescent times (> 80 ka) and old in situ diversification (> 1 Ma) point to the persistence of populations over multiple glacio-eustatic cycles. We provide data suggesting demographic expansion during sea-level high stands. Regional connectivity was lower, and cryptic differentiation higher in lecithotrophs than in planktotrophs. Main conclusions The analytical framework based on a biodiversity survey makes it possible to identify evospots by assessing the potential of a region to maintain and generate biodiversity and by evaluating the evolutionary processes and potential drivers at play.

Microsatellite DNA markers were isolated in an amphidromous goby (Sicyopterus lagocephalus) from a partial genomic library enriched for AC repeats. Eight microsatellites were highly polymorphic with six to 33 alleles per locus and expected heterozygosities ranging from 0.53 to 0.97. Cross-species amplifications were performed within the sub-family Sicydiinae by genotyping individuals from two species of the genus Cotylopus. Some of these loci were successfully amplified and showed polymorphism in the second genus.

Despite their importance in marine biodiversity, invertebrates are far less studied than vertebrates. Given the current global biodiversity crisis and insufficient taxonomic resources, sustained efforts need to be undertaken to assess species diversity, especially in the highly threatened 'biodiversity hotspots'. Reunion is a young volcanic island lying in the Mascarene Islands (south-western Indian Ocean, SWIO), a marine biodiversity hotspot. A substantial sampling effort was conducted around Reunion Island to document shallow water reef-associated ophiuroid (brittle-stars) diversity, a class recognised as the most diverse among echinoderms. A total of 33 species were documented, increasing the known species richness of the island by 56%. Findings include 15 new records for Reunion, 11 for the Mascarene Islands and 8 for the Indian Ocean. The most diverse family was Ophiocomidae, a family of large, abundant and conspicuous tropical species. Even in this well studied family, a new species was revealed by this survey. Morphological variants together with DNA sequence variations within several species revealed cryptic species. We compared our results with the known fauna of other Mascarene Islands and discuss biogeographic implications for the region.

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (

Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing.

Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa., BMC Evolutionary Biology, 10, ISSN:1471-2148

Sicyopterus lagocephalus post-larvae migrating in Mascarene Archipelago rivers, La Réunion Island, provide an important food source to local populations and fishing activity has a socioeconomic impact. Improved knowledge of the life traits and the characterisation of post-larval stages should enable a better understanding of physiological changes triggering migratory behaviour. It would also help to explain the recruitment processes to managers and to implement conservation measures for stock management. Sicyopterus lagocephalus is an amphidromous fish: adults live in rivers, but larvae are carried to the sea after hatching. The present study characterised the metamorphosis and post-larval stages of Sicyopterus lagocephalus during river recolonisation on La Réunion Island. The results show that cranium reorganisation and pectoral fins transformation are part of the first and major transformations and are completed less than 2 weeks after freshwater colonisation (post-larval stages PL1 and PL2). These transformations, mobilising all the available calcium, seem to be critical for survival in their new environment. Individuals then progressively acquire pigmentation, complete scalation and the fork at the end of the caudal fin disappears (juvenile stages J1 and J2). The end of the recruitment phase takes place 21 to 28 days after entering the river mouth, when territorial behaviour appears.

International audience; The 2 amphidromous gobiids Sicyopterus lagocephalus and Cotylopus acutipinnis from La Réunion Island (Mascarene archipelago, south-western Indian Ocean) are heavily exploited by traditional fisheries during their river colonisation. Traits of their oceanic larval life were investigated to better understand the complex life cycle of these fishes. Age estimates were established using otolith increment counts and an alizarin complexon validation method. Larval duration was longer for the widespread S. lagocephalus (133 to 266 d; mean 199 ± 33 d) than for the endemic C. acutipinnis (78 to 150 d; mean 101 ± 14 d), which reflects their distributional ranges. For both species, no correlation was established between age and size, suggesting a decrease in growth during the larval phase. From the back-calculated birth dates, all S. lagocephalus of a major colonisation episode (December 2002) were hatched during the cool season. All results are discussed in terms of the recruitment origins of S. lagocephalus and C. acutipinnis within the Mascarenes. Recognition of the differences in larval life traits is essential for proposing both management and conservation measures for each species.

International audience; Sicyopterus lagocephalus is a Gobiidae Sicydiinae (Teleostei) thought to inhabit Indo-Pacific island rivers from Comoros Islands in the Indian Ocean to Australs Islands (French Polynesia) in the Pacific Ocean. Its biological cycle comprises a marine planctonic larval phase of several months allowing it to migrate from island to island, but the other species of the genus, with such a larval stage, have generally a more restricted range and are often endemic. To understand the organisation of a species with such a wide distribution, mtDNA cytochrome b sequences were amplified for 55 specimens of this genus covering most of its distribution range together with six close endemic species and other gobiids used as outgroups. The main result is the confirmation of the ubiquity of S. lagocephalus that occurs over a range of 18,000 km in the Indian and Pacific Oceans. Two clades were identified within this species, one clustering most of French Polynesian haplotypes and the other clustering most of Mascarene (including Comoros) haplotypes. The overall pattern of distribution and phylogenetic relationship suggests that the lineages leading to endemic species originated earlier than S. lagocephalus. This latter seems to be a secondary migrant species, having colonised both Indian and Pacific Oceans with a few exceptions, situated at the border of the range (Madagascar, Marquesas, Rapa). According to the results, the phylogeny of the Sicyopterus group, the age of the different lineages and the past history of the colonisation of the Indo-Pacific islands are discussed.

International audience; In the subfamily Sicydiinae of the family Gobiidae, the species Sicyopterus lagocephalus is one of the common amphidromous fish inhabiting island freshwaters in a large intertropical area, widespread from the Comoros archipelago to the Austral Islands. Eight of the main perennial rivers of La Réunion Island (Mascarene Islands) were sampled in 2000, in order to describe their population genetic structure. A total of 267 adult specimens of S. lagocephalus were screened for 14 enzymatic systems providing 15 presumptive loci, 11 of them being polymorphic. Four other loci were useful as diagnostic markers between S. lagocephalus and Cotylopus acutipinnis, a similar, closely related sympatric species. Both species constitute an economic resource locally called “bichique”. The focus of this study, S. lagocephalus, accounts for the majority of the bichique. The results clearly showed a genetic homogeneity among the eight samples (Fst tests). Within-samples tests (Fis) indicated, in general, a heterozygote deficiency. The multidimensional diagrams (CA) describe an overall structure composed of two main subgroups. This structure was not confirmed in a 2001 sampling. The interpretation of the results takes into account the biological life cycle of this species, characterized by a planktonic phase, from hatching to recruitment, followed by a freshwater life of the adults. All the samples in the survey belong to a single pool. However, the young fish entering the rivers are probably of complex origin. We did not find any isolation between rivers and this result should be considered when conservation measures are taken to prevent overfishing.

The ability of Tonkean macaques (Macaca tonkeana) to deceive partner about the location of hidden food was investigated in 4 males belonging to a group raised in a 2-acre park. Before releasing subjects in the search task, the experimenter prompted 1 of the subjects to observe where the bait was hidden. The authors found that when informed, higher ranking subjects did not significantly alter their search patterns whether tested alone or in pairs. The same held for subordinates belonging to pairs with weak dominance asymmetry. To the contrary, strongly dominated subordinates modified the number of pauses when searching in pairs. They used behavioral tactics such as avoiding being followed, stopping when being watched, or taking a wrong direction. Information withholding might be acommon event in macaques.