Papers by Lapo Ragionieri
Estuarine, Coastal and Shelf Science, 2008
Keywords: bioaccumulation heavy metals Mediterranean basin mean d 2 microsatellites natural marin... more Keywords: bioaccumulation heavy metals Mediterranean basin mean d 2 microsatellites natural marine populations a b s t r a c t
The FEBS journal, Jan 22, 2014
Heterologous protein production is a key technology for biotechnological, health sciences and man... more Heterologous protein production is a key technology for biotechnological, health sciences and many other research fields. Various approaches have been developed for its optimization, but the research emphasis has been on optimization of protein yield rather than protein quality. In this study, we have established a workflow for synthetic gene optimization for heterologous protein expression that combines bioinformatics, laboratory experiments, mass spectrometry and statistical analysis. Two gene primary structure analysis platforms, Anaconda and EuGene, and multivariate optimization methods were employed to re-design the Plasmodium falciparum lysyl-tRNA synthetase gene for optimal expression in Escherichia coli. Synthetic genes were expressed from common vectors, and amino acid mis-incorporations in the expressed proteins were detected and quantified using mass spectrometry. The association between the identified amino acid mis-incorporations and 23 gene variables was then analysed....
Until recently, it was generally believed that marine species with planktonic larval dispersal sh... more Until recently, it was generally believed that marine species with planktonic larval dispersal should be genetically homogeneous across their geographic range. Nowadays, however, there is increasing evidence for genetically structured marine populations among larval-dispersed species, and thus a higher degree of intraspecific local variability than expected. The sometimes very complex patterns of intraspecific genetic differentiation may be due to historical environmental factors related to habitat, currents and sea level fluctuations, and/or to present-day species-specific traits and ecological factors. Studies on population genetic structure are commonly based on the geographical distribution of mitochondrial haplotypes or, alternatively, on polymorphism at microsatellite loci. These genetic markers have different molecular and evolutionary properties, and, as a consequence, they may reveal different distribution patterns of the recorded genetic variation. Mitochondrial DNA is a h...
The Raffles bulletin of zoology
Biological Invasions, 2013
Biological Journal of the Linnean Society, 2013
Carcinus aestuarii Nardo, 1847 is a widespread coastal crab species throughout the Mediterranean ... more Carcinus aestuarii Nardo, 1847 is a widespread coastal crab species throughout the Mediterranean Sea with a pelagic larval phase. This species tolerates a wide range of environmental conditions and typically inhabits fragmented habitats, such as embayments, lagoons and estuaries. It is therefore a good candidate species for studying and testing different phylogeographical hypotheses in the Mediterranean Sea. By contrast to its Atlantic sister species, Carcinus maenas, studies on the population genetic structure of C. aestuarii in its native range are still scarce. In the present study, specimens from along the European Mediterranean Sea were collected and DNA-sequenced and analyses were applied to discriminate between present day and historical factors influencing the population genetic structure of this species. The results obtained demonstrate the existence of two genetically distinct geographical groups, corresponding to the eastern and western Mediterranean, with further subdivision within the East Mediterranean Basin. A strong asymmetric gene flow was recorded toward the Eastern Basin, which may play a crucial role in shaping the present day biogeographical patterns of this species and potentially other sympatric ones with pelagic larvae.
Molecular Phylogenetics and Evolution, 2009
The presence of boundaries to dispersal has been recently documented for many Indo-West Pacific (... more The presence of boundaries to dispersal has been recently documented for many Indo-West Pacific (IWP) species with planktonic propagules and a widespread distribution. We studied the phylogeography of the mangrove crab Neosarmatium meinerti (Brachyura: Sesarmidae) and the phylogenetic relationship to its presumed sister species N. fourmanoiri in the IWP in order to compare intraspecific with interspecific diversity. Portions of the mitochondrial genes 16S and CoxI were sequenced for 23 specimens of N. meinerti and 5 N. fourmanoiri, while a fragment of the 28S was obtained for a subset of specimens. Genetic data are supplemented by morphometric and based on 37 adult males of N. meinerti and 9 males of N. fourmanoiri.
Hydrobiologia, 2015
Most intertidal brachyurans produce planktonic larvae which develop pelagically and, after a cert... more Most intertidal brachyurans produce planktonic larvae which develop pelagically and, after a certain time in the ocean, migrate towards the habitats that they will eventually settle in. One of the main physical processes affecting larval release and settlement in species inhabiting estuaries and mangroves is the tidal regime. In this study, we investigated whether patterns of settlement of brachyuran larvae at four sites (differing in tidal inundation and crab zonation) of a Kenyan mangrove were affected by the diurnal and lunar cycle of the tide. We collected megalopae at the four sites twice a day throughout two lunar months. Settlement differed at the four sites: at the subtidal site (the main creek within the forest) megalopae arrived during diurnal and nocturnal neap and spring tides, while at the three sites within the forest settlement occurred only at spring tide periods. Specific differences among these latter sites existed in terms of full versus new moon spring tides and, to a smaller extent, with diurnal period. Our results show that larval settlement in mangrove forests takes place at both landward and seaward belts and is a temporally complex event, driven by tidal cycles, but also in synergy with other factors.
Keywords: bioaccumulation heavy metals Mediterranean basin mean d 2 microsatellites natural marin... more Keywords: bioaccumulation heavy metals Mediterranean basin mean d 2 microsatellites natural marine populations a b s t r a c t
Estuarine, Coastal and Shelf Science, 2010
Most marine organisms are characterized by at least one planktonic phase during their life histor... more Most marine organisms are characterized by at least one planktonic phase during their life history, potentially allowing interconnection of populations separated by several hundred kilometers. For many years, the idea that marine species are genetically homogenous throughout their range of distribution, due to passive larval transport, has been a paradigm. Nowadays, a growing number of studies underline the existence of boundaries in the marine realm and highlight how larval dispersal is a complex process depending on biotic as well as abiotic factors. Marine fragmented habitats, such as atolls, mangroves and estuaries, are optimal systems for investigating the marine dispersion process under a metapopulation approach, since populations can be geographically defined a priori as opposed to those occupying open marine environments. Within this frame, the present paper investigates the population genetic structure and the demographic history of the mangrove crab Neosarmatium meinerti within the western Indian Ocean by partial sequences of the mitochondrial DNA cytochrome oxidase subunit I. A total of 167 specimens were sampled from six mangrove sites distributed along the East African coast, from Kenya to South Africa, also including a mangrove forest located on Mahé Island, Seychelles. A sharp genetic break between the mainland and the Seychelles is recorded, revealing the existence of two historically distinct groups that can be defined as independent evolutionary units. Gene flow along the East African coast appears to be high enough to form a single metapopulation, probably by means of stepping stone populations. Otherwise, this mainland metapopulation is currently under expansion through a gradual moving front from the subtropical toward the equatorial populations.
Estuarine, Coastal and Shelf Science, 2010
The increasing exploitation of mangrove forests, without any sustainable planning, has been serio... more The increasing exploitation of mangrove forests, without any sustainable planning, has been seriously compromising the survival of this ecosystem and of its exclusive resources. Scylla serrata is one of the most commercially exploited crabs inhabiting mangroves and estuaries of the Indo-Pacific region. This species is extensively harvested, mainly for selling to the tourist market, and, as a consequence, its populations are in constant decline. The aim of the present study was to assess the level of genetic exchange of S. serrata within the Western Indian Ocean (WIO), using a population genetic structure approach. To achieve this goal, we reconstructed the intra-specific geographic pattern of genetic variation by partial sequencing the mitochondrial DNA cytochrome oxidase subunit I, in samples from seven mangrove sites of the WIO. Our data set then encompassed all the sequences for the same genetic marker deposited in Genbank and corresponding to samples from South East Asia, Australia and some Pacific Islands: this allowed us to estimate the level of connectivity among S. serrata populations within its distribution area.
Marine Ecology Progress Series, 2013
The genetic connectivity level of the benthic crab Pachygrapsus marmoratus was assessed within th... more The genetic connectivity level of the benthic crab Pachygrapsus marmoratus was assessed within the Tuscan Archipelago, an area between the Ligurian and Tyrrhenian Seas, Italy. The archipelago comprises 7 islands lying inside the largest marine protected area of the Mediterranean Sea. We genotyped a total of approximately 230 individuals from 8 populations (4 protected and 4 unprotected) at 8 microsatellites. Overall, our results showed a clear partitioning of genetic variation within this area; all populations were separated from one another, except the 2 southernmost islands. This genetic subdivision could be due to a 'sweepstakes reproductive effect' (i.e. only a small proportion of the available gene pool successfully contributes to the replenishment of each population). Furthermore, the lack of a pattern of isolation by distance, coupled with a low percentage of individuals assigned to their own populations, indicates that retention of larvae near the parent population is unlikely to be the main cause of the recorded genetic structure. However, we also found evidence of past demographic events in all populations, which may have played a pivotal role in shaping the recorded pattern of intraspecific differentiation. Finally, we did not detect any difference in the level of genetic variation between populations that were protected (i.e. experiencing less human pressure) and those that were unprotected. This suggests that, from a genetic point of view, the effects of protection have not yet been demonstrated.
Estuarine Coastal and Shelf Science
Most marine organisms are characterized by at least one planktonic phase during their life histor... more Most marine organisms are characterized by at least one planktonic phase during their life history, potentially allowing interconnection of populations separated by several hundred kilometers. For many years, the idea that marine species are genetically homogenous throughout their range of distribution, due to passive larval transport, has been a paradigm. Nowadays, a growing number of studies underline the existence of boundaries in the marine realm and highlight how larval dispersal is a complex process depending on biotic as well as abiotic factors. Marine fragmented habitats, such as atolls, mangroves and estuaries, are optimal systems for investigating the marine dispersion process under a metapopulation approach, since populations can be geographically defined a priori as opposed to those occupying open marine environments. Within this frame, the present paper investigates the population genetic structure and the demographic history of the mangrove crab Neosarmatium meinerti within the western Indian Ocean by partial sequences of the mitochondrial DNA cytochrome oxidase subunit I. A total of 167 specimens were sampled from six mangrove sites distributed along the East African coast, from Kenya to South Africa, also including a mangrove forest located on Mahé Island, Seychelles. A sharp genetic break between the mainland and the Seychelles is recorded, revealing the existence of two historically distinct groups that can be defined as independent evolutionary units. Gene flow along the East African coast appears to be high enough to form a single metapopulation, probably by means of stepping stone populations. Otherwise, this mainland metapopulation is currently under expansion through a gradual moving front from the subtropical toward the equatorial populations.
The Tavolara archipelago (NE Sardinia, Italy), which possibly holds over 50 % of the world popula... more The Tavolara archipelago (NE Sardinia, Italy), which possibly holds over 50 % of the world population of breeding Yelkouan Shearwaters Puffinus yelkouan, was infested by black rats Rattus rattus. An action plan was developed in order to decrease the impact of rats. In October 2008, rat eradication of Molara Island has been achieved by aerial distribution of poisoned baits while ground-based eradication was carried out on three islets. Post eradication monitoring has shown that the operations were successful. However rats were found again on Molara Island 21 months after eradication. Genetic analysis showed that they were from the mainland population. Thus, most probably they have been intentionally introduced by man.
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Papers by Lapo Ragionieri