[Show abstract][Hide abstract] ABSTRACT: Background
The freshwater snail Biomphalaria acts as the intermediate host of Schistosoma mansoni, a globally important human parasite. Understanding the population structure of intermediate host species can elucidate transmission dynamics and assist in developing appropriate control methods.Methods
We examined levels of population genetic structure and diversity in 29 populations of Biomphalaria choanomphala collected around the shoreline of Lake Victoria in Uganda, Kenya and Tanzania, where S. mansoni is hyper-endemic. Molecular markers were utilized to estimate the degree to which snail populations are genetically differentiated from one another.ResultsHigh levels of snail genetic diversity were found coupled with evidence of geographically-determined population structure but low levels of local inbreeding. The data are consistent with an effect of schistosome infection on population structure of intermediate host snails, but other factors, such as habitat and historical demographic changes, could also be important determinants of the degree of population genetic structure in Biomphalaria choanomphala.Conclusions
The low stratification of populations and high genetic diversity indicates potentially less local compatibility with intermediate snail populations than previously theorized, and highlights the importance of coordinated parasite control strategies across the region.
[Show abstract][Hide abstract] ABSTRACT: Here we present an evaluation of several methods for extracting DNA from within intact foraminiferal shells. We tested 12 lysis buffers under carefully optimised incubation conditions, evaluating their success in terms of efficiency in evacuating cellular material, crude DNA yield, PCR success, and final shell integrity. A number of the buffers tested produced excellent results. The most successful method utilized a lysis buffer containing Sodium N-lauroyl sarcosine, Guanidinium isothiocyanate, Isopropanol, TRIS and NaCl, incubated at 75°C for 24 hours, followed by chloroform extraction and ethanol precipitation. High yields of DNA were produced, with no signs of PCR inhibition, and the foraminiferal shells were left completely intact. Retaining the shell of individual specimens presents a significant advance, allowing for direct comparisons between shell morphology and genotype data, which could greatly enhance the utility of foraminifera as palaeoproxies of past climate change.
[Show abstract][Hide abstract] ABSTRACT: Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates of evolution appear to cause phylogenetic incongruence in protein-coding sequence comparisons between vertebrate taxa. Our results support the hypothesis that germ plasm liberates constraints on somatic development and that enhanced evolvability drives the evolution of germ plasm.
[Show abstract][Hide abstract] ABSTRACT: A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
[Show abstract][Hide abstract] ABSTRACT: A high degree of intraspecific variation, both genetic and in shell morphology, of the operculate land snail Cyclophorus fulguratus (Pfeiffer, 1854) suggests that its classification as a single species warrants reconsideration. We sequenced two nuclear (18S and 28S) and two mitochondrial (16S and COI) genes of 46 C. fulguratus specimens and used them to estimate the phylogeny and to determine the validity of species boundaries. Molecular phylogenetic analyses revealed the presence of three lineages corresponding to three geographically disjunctive populations of C. fulguratus in Thailand. Likelihood tests of topologies significantly supported the non-monophyly of the C. fulguratus-complex and Bayesian species delimitation analysis significantly supported the potential representation as distinct species of these three lineages. Discriminant function analysis based on geometric-morphometrics of shell shape allowed for significant distinction of these three candidate species, although they revealed a considerable degree of overlap of shell shape reflecting their crypsis morphologically. The diagnostic characters are provided by color pattern, pattern of protoconch and pattern of jaw. In conclusion, the results support that the C. fulguratus s.l., as currently recognized, consists of three distinct species in Thailand: C. fulguratus s.s., C. rangunensis and C. abditus sp.nov., which are described herein.
PLoS ONE 01/2014; 9(10):e109785. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Giant African Land Snail, Achatina ( = Lissachatina) fulica Bowdich, 1822, is a tropical crop pest species with a widespread distribution across East Africa, the Indian subcontinent, Southeast Asia, the Pacific, the Caribbean, and North and South America. Its current distribution is attributed primarily to the introduction of the snail to new areas by Man within the last 200 years. This study determined the extent of genetic diversity in global A. fulica populations using the mitochondrial 16S ribosomal RNA gene. A total of 560 individuals were evaluated from 39 global populations obtained from 26 territories. Results reveal 18 distinct A. fulica haplotypes; 14 are found in East Africa and the Indian Ocean islands, but only two haplotypes from the Indian Ocean islands emerged from this region, the C haplotype, now distributed across the tropics, and the D haplotype in Ecuador and Bolivia. Haplotype E from the Philippines, F from New Caledonia and Barbados, O from India and Q from Ecuador are variants of the emergent C haplotype. For the non-native populations, the lack of genetic variation points to founder effects due to the lack of multiple introductions from the native range. Our current data could only point with certainty to the Indian Ocean islands as the earliest known common source of A. fulica across the globe, which necessitates further sampling in East Africa to determine the source populations of the emergent haplotypes.
PLoS ONE 01/2014; 9(9):e105151. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Operculate land snails of the genus Cyclophorus are distributed widely in sub-tropical and tropical Asia. Shell morphology is traditionally used for species identification in Cyclophorus but their shells exhibit considerable variation both within and between populations; species limits have been extremely difficult to determine and are poorly understood. Many currently recognized species have discontinuous distributions over large ranges but geographical barriers and low mobility of snails are likely to have led to long periods of isolation resulting in cryptic speciation of allopatric populations. As a contribution towards solving these problems, we reconstructed the molecular phylogeny of 87 Cyclophorus specimens, representing 29 nominal species (of which one was represented by four subspecies), plus three related out-group species. Molecular phylogenetic analyses were used to investigate geographic limits and speciation scenarios. The analyses of COI, 16S rRNA and 28S rRNA gene fragments were performed using neighbour-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. All the obtained phylogenetic trees were congruent with each other and in most cases confirmed the species level classification. However, at least three nominate species were polyphyletic. Both C. fulguratus and C. volvulus appear to be species complexes, suggesting that populations of these species from different geographical areas of Thailand are cryptic species. C. aurantiacus pernobilis is distinct and likely to be a different species from the other members of the C. aurantiacus species complex.
Molecular Phylogenetics and Evolution 09/2013; · 4.07 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Genetic studies of the Foraminifera provide valuable insights into marine speciation and biogeography, yet the discovery of vitally needed new genetic markers for this important group is being severely limited by an extreme lack of genetic data. The establishment of a laboratory culture from a single, asexually reproducing foraminifer, will be essential to provide enough pooled genetic material from these unicellular organisms, to facilitate full genome sequencing and genetic marker discovery, using next-generation sequencing techniques.
The aim of this study was to develop a simple and inexpensive method of culturing benthic foraminifera, via asexual reproduction, in a controlled laboratory environment. Individual specimens of the benthic foraminfer Cornuloculina balkwilli (MacFadyen) were placed in 7 cm plastic beakers, containing 50 ml natural seawater, filtered to 0.2 mum, and kept at 23[degree sign]C, with a 12-hour light/dark cycle, and fed weekly on a mixed algal diet of Dunaliella tertiolecta and Phaeodactylum tricornutum. Asexually derived cultures were successfully established from 4 specimens of Cornuloculina balkwilli, originally added to the culture vessels as immature specimens. Many thousands of individuals were present after 6 months.
The method presented here demonstrates that only basic laboratory equipment is required to establish and maintain a thriving culture of the benthic foraminfer, C. balkwilli, from a single asexually reproducing specimen, providing an excellent source of genetic material for use in next generation sequencing. The method is easily reproducible and will greatly aid in the discovery of critically needed new genetic markers in the Foraminifera. It also highlights C. balkwilli as a good candidate species for use in the field of environmental micropaleontology.
[Show abstract][Hide abstract] ABSTRACT: Ecological processes are increasingly being viewed as an important mode of diversification in the marine environment, where the high dispersal potential of pelagic organisms, and a lack of absolute barriers to gene flow may limit the occurrence of allopatric speciation through vicariance. Here we focus on the potential role of ecological partitioning in the diversification of a widely distributed group of marine protists, the planktonic foraminifera. Sampling was conducted in the tropical Arabian Sea, during the southwest (summer) monsoon, when pronounced environmental conditions result in a strong disparity in temperature, salinity and productivity between distinct northern and southern water masses.
We uncovered extensive genetic diversity within the Arabian Sea planktonic foraminifera, identifying 13 morphospecies, represented by 20 distinct SSU rRNA genetic types. Several morphospecies/genetic types displayed non-random biogeographical distributions, partitioning between the northern and southern water masses, giving a strong indication of independent ecological adaptations.
We propose sea-surface primary productivity as the main factor driving the geographical segregation of Arabian Sea planktonic foraminifera, during the SW monsoon, with variations in symbiotic associations possibly playing a role in the specific ecological adaptations observed. Our findings suggest that ecological partitioning could be contributing to the high levels of 'cryptic' genetic diversity observed within the planktonic foraminifera, and support the view that ecological processes may play a key role in the diversification of marine pelagic organisms.
[Show abstract][Hide abstract] ABSTRACT: Lake Victoria is a known hot-spot for Schistosoma mansoni, which utilises freshwater snails of the genus Biomphalaria as intermediate hosts. Different species of Biomphalaria are associated with varying parasite compatibility, affecting local transmission. It is thought that two species, B. choanomphala and B. sudanica, inhabit Lake Victoria; despite their biomedical importance, the taxonomy of these species has not been thoroughly examined. This study combined analysis of morphological and molecular variables; the results demonstrated that molecular groupings were not consistent with morphological divisions. Habitat significantly predicted morphotype, suggesting that the different Lake Victorian forms of Biomphalaria are ecophentoypes of one species. The nomenclature should be revised accordingly; the names B. choanomphala choanomphala and B. c. sudanica are proposed. From a public health perspective, these findings can be utilised by policy-makers for better understanding of exposure risk, resulting in more effective and efficient control initiatives.
PLoS ONE 01/2011; 6(10):e26563. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Evolution of planktic organisms from benthic ancestors is commonly thought to represent unidirectional expansion into new ecological domains, possibly only once per clade. For foraminifera, this evolutionary expansion occurred in the Early-Middle Jurassic, and all living and extinct planktic foraminifera have been placed within 1 clade, the Suborder Globigerinina. The subsequent radiation of planktic foraminifera in the Jurassic and Cretaceous resulted in highly diverse assemblages, which suffered mass extinction at the end of the Cretaceous, leaving an impoverished assemblage dominated by microperforate triserial and biserial forms. The few survivor species radiated to form diverse assemblages once again in the Cenozoic. There have, however, long been doubts regarding the monophyletic origin of planktic foraminifera. We present surprising but conclusive genetic evidence that the Recent biserial planktic Streptochilus globigerus belongs to the same biological species as the benthic Bolivina variabilis, and geochemical evidence that this ecologically flexible species actively grows within the open-ocean surface waters, thus occupying both planktic and benthic domains. Such a lifestyle (tychopelagic) had not been recognized as adapted by foraminifera. Tychopelagic are endowed with great ecological advantage, enabling rapid recolonization of the extinction-susceptible pelagic domain from the benthos. We argue that the existence of such forms must be considered in resolving foraminiferal phylogeny.
Proceedings of the National Academy of Sciences 08/2009; 106(31):12629-33. · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Fossil planktic foraminifers in the ocean sediments play an unparalleled role in our understanding of the oceanographic environment in the past. An in depth knowledge of their diversity, ecology and biogeography in the modern ocean lies central to the interpretation of the fossil assemblages. In comparison with their benthic counterparts, planktic foraminifera have a very limited diversity of around fifty extant morphospecies. Their morphospecies diversity peaks in the sub-tropics and decreases steeply towards the poles. Traditional species concepts have partitioned morphological types into distinct species (morphospecies) based on test shape, but genetic studies show that individual morphospecies are actually complexes of several discrete genetic types (genotypes). Many of these genotypes have distinct ecologies and novel adaptations that are consistent with species-level classification, indicating that the true diversity of planktic foraminifers has been greatly underestimated. Although planktic foraminifera are clearly capable of long-distance dispersal, they may be constrained by both physical and ecological barriers that vary according to the evolutionary history and ecology of the individual genotypes within a morphospecies. These differences lead to diverse biogeographies. Here, we provide an overview of the genetic and biogeographic data available to date for the planktic foraminifera and present global biogeographies highlighting the distribution of genetic types in the eight planktic foraminiferal morphospecies for which detailed molecular evidence is available.
[Show abstract][Hide abstract] ABSTRACT: We have developed a molecular method using PCR-direct sequencing to identify the infective 3rd juvenile stage of Angiostrongylus cantonensis, a nematode parasite of rodents that can accidentally infect humans and cause eosinophilic meningitis. We demonstrate that the 5' end of the small subunit (SSU) ribosomal (r) RNA gene is a suitable marker to identify A. cantonensis and distinguish it from other closely related Angiostrongylus species. When the SSU rRNA marker was employed on nematode populations extracted from the black slug Laevicaulis altae collected in 2 test sites in the Philippines, the infective 3rd juvenile stage A. cantonensis was detected without difficulty. The phylogenetic position of other non-angiostrongylid nematodes isolated was also determined. The molecular technique developed in this study provides a rapid and accurate method for the identification of A. cantonensis when morphological identification proves difficult or inadequate.
[Show abstract][Hide abstract] ABSTRACT: The high-latitude planktonic foraminifera have proved to be particularly useful model organisms for the study of global patterns of vicariance and gene flow in the oceans. Such studies demonstrate that gene flow can occur over enormous distances in the pelagic marine environment leading to cosmopolitanism but also that there are ecological and geographical barriers to gene flow producing biogeographic structure. Here, we have undertaken a comprehensive global study of genetic diversity within a marine protist species, the high-latitude planktonic foraminiferan Neogloboquadrina pachyderma. We present extensive new data sets from the North Pacific and Arctic Oceans that, in combination with our earlier data from the North Atlantic and Southern Oceans, allow us to determine the global phylogeography of this species. The new genetic data reveal a pattern of Arctic circumpolar isolation and bipolar asymmetry between the Atlantic and Pacific Oceans. We show that the ancestry of North Pacific N. pachyderma is relatively recent. It lies within the upwelling systems and subpolar waters of the Southern Hemisphere and remarkably not within the neighboring Arctic Ocean. Instead, the Arctic Ocean population forms a genetic continuum with the North Atlantic population, which became isolated from the southern populations much earlier, after the onset of Northern hemisphere glaciation. Data from the planktonic foraminiferal morphospecies Globigerina bulloides is also introduced to highlight the isolation and endemism found within the subpolar North Pacific gyre. These data provide perspective for interpretation and discussion of global gene flow and speciation patterns in the plankton.
Proceedings of the National Academy of Sciences 04/2007; 104(12):5002-7. · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Specimens of the biserial planktonic foraminiferal genus Streptochilus were collected 540 nautical miles offshore in the central Arabian Sea during the summer monsoon of 2003. Samples were collected from 5m water depth in waters with an average depth of 3,500 metres. All living specimens had bright orange coloured cytoplasm and sizes ranged from juvenile to fully mature. Ancestral relationships were determined by comparing their small subunit ribosomal DNA sequences with those from closely related and morphologically similar taxa. Living benthic foraminifers are commonly found suspended in the plankton in high energy turbulent waters, particularly over shallow shelf regions. Expatriation into the open ocean may also occur providing there is sufficient turbulence to keep them in suspension. In addition, there is also the possibility of propagule transport into the open ocean. Whether Streptochilus is solely planktonic has been continually questioned and we explore the life history of Streptochilus using molecular, morphological, ecological and geochemical evidence to find clues to its ancestry and ecological habit.
TMS joint Foraminifera and Nannofossil Meeting, Anger; 01/2007
[Show abstract][Hide abstract] ABSTRACT: We present new data on genotypic differences and biogeographic
distribution of coiling types in the living planktonic foraminiferal
morphospecies Neogloboquadrina pachyderma. The genetic evidence
demonstrates that coiling direction in N. pachyderma is a genetic trait,
heritable through time, and is not a morphological feature reflecting
ecophenotypic variation. The two opposite coiling morphotypes appear to
have diverged during the late Miocene, and they have distinctly
different ecologies. In combination with fossil evidence, biogeography,
and ecology the degree of genetic distinction between the two coiling
types of N. pachyderma strongly implies that they should be considered
different species. We propose the adoption of the widely recognized name
N. incompta for the right coiling morphospecies. The genetic evidence
also demonstrates a low level (<3%) of aberrant coiling associated
with both morphotypes. The abundance of these aberrant specimens has no
relationship with the environment. These findings have important
consequences for the use of N. pachyderma and N. incompta as
paleoceanographic signal carriers in polar and subpolar waters.