L Zane

Publications of L Zane

• Phylogenetic relationships and demographic histories of the Atherinidae in the Eastern Atlantic and Mediterranean Sea re-examined by Bayesian inference.

  Authors: J M Pujolar, L Zane, L Congiu

  Molecular phylogenetics and evolution. 03/2012;

  The aim of our study is to examine the phylogenetic relationship, divergence times and demographic history of the five close-related Mediterranean and North-eastern Atlantic species/forms of AtherinaThe aim of our study is to examine the phylogenetic relationship, divergence times and demographic history of the five close-related Mediterranean and North-eastern Atlantic species/forms of Atherina using the full Bayesian framework for species tree estimation recently implemented in ∗BEAST. The inference is made possible by multilocus data using three mitochondrial genes (12S rRNA, 16S rRNA, control region) and one nuclear gene (rhodopsin) from multiple individuals per species available in GenBank. Bayesian phylogenetic analysis of the complete gene dataset produced a tree with strong support for the monophyly of each species, as well as high support for higher level nodes. An old origin of the Atherina group was suggested (19.2MY), with deep split events within the Atherinidae predating the Messinian Salinity Crisis. Regional genetic substructuring was observed among populations of A. boyeri, with AMOVA and MultiDimensional Scaling suggesting the existence of five groupings (Atlantic/West Mediterranean, Adriatic, Greece, Black Sea and Tunis). The level of subdivision found might be consequence of the hydrographic isolation within the Mediterranean Sea. Bayesian inference of past demographic histories showed a clear signature of demographic expansion for the European coast populations of A. presbyter, possibly linked to post-glacial colonizations, but not for the Azores/Canary Islands, which is expected in isolated populations because of the impossibility of finding new habitats. Within the Mediterranean, signatures of recent demographic expansion were only found for the Adriatic population of A. boyeri, which could be associated with the relatively recent emergence of the Adriatic Sea.

• Inferring the demographic history of the Adriatic Flexopecten complex.

  Authors: J M Pujolar, T Marčeta, C Saavedra, M Bressan, L Zane

  Molecular phylogenetics and evolution. 11/2010; 57(2):942-7.

  Phylogenetic analysis of DNA sequences can be a useful tool in taxonomical studies, which has important implications in terms of species traceability. The aim of our study is to solve the controversyPhylogenetic analysis of DNA sequences can be a useful tool in taxonomical studies, which has important implications in terms of species traceability. The aim of our study is to solve the controversy regarding the taxonomical status of the Flexopecten group, which includes two putative sister species (F. glaber and F. proteus) that co-occur in the Adriatic Sea and are clearly distinguishable on the basis of morphometric characters. Our molecular analysis using three mitochondrial genes (COI, 12S rRNA and 16S rRNA) and one nuclear gene (Histone H3) suggest that F. glaber and F. proteus are the same species, as evidenced by both putative species appearing mixed in all genetic trees with no clustering according to species. Using a Bayesian approach, we inferred the demographic history of the Flexopecten group, which suggests that first F. glaber occurred in the Mediterranean, then F. glaber colonized the Adriatic sometime in the last 18,000 years, and finally the F. proteus morph appeared only recently in the Adriatic Sea. We propose F. proteus to be synonymized with F. glaber, which should have priority and be used in the future.

• Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010.

  Authors: Cynthia M Anderson, Gallego J Aparicio, Alain R Atangana, Jean Beaulieu, M W Bruford, Forrest Cain, T Campos, A Cariani, M A Carvalho, Nan Chen [......] Huan L Wang, LE Wang, Rémi A Wattier, Maren Wellenreuther, Cong X Xie, L Zane, Xiu J Zhang, Yong Zhang, Zhimeng Zhuang, M I Zucchi

  Molecular ecology resources. 05/2010; 10(3):576-579.

  This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, AmblyrajaThis article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.

• Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010

  Authors: C. M. Anderson, G. J. Aparicio, A. R. Atangana, J. Beaulieu, M. W. Bruford, F. Cain, T. Campos, A. Cariani, M. A. Carvalho, N. Chen [......] L. Wang, R. A. Wattier, M. Wellenreuther, C. X. Xie, L. Zane, X. J. Zhang, Y. Zhang, Z. M. Zhuang, M. I. Zucchi, Dev Mol Ecology Resources Primer

  Molecular Ecology Resources. 01/2010; 10(3):576-579.

  This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, AmblyrajaThis article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.

• Genetic variability is unrelated to growth and parasite infestation in natural populations of the European eel (Anguilla anguilla).

  Authors: J M Pujolar, D Bevacqua, F Capoccioni, E Ciccotti, G A De Leo, L Zane

  Molecular ecology. 10/2009;

  Abstract Positive correlations between individual genetic heterozygosity and fitness-related traits (HFCs) have been observed in organisms as diverse as plants, marine bivalves, fish or mammals. HFCsAbstract Positive correlations between individual genetic heterozygosity and fitness-related traits (HFCs) have been observed in organisms as diverse as plants, marine bivalves, fish or mammals. HFCs are not universal and the strength and stability of HFCs seem to be variable across species, populations and ages. We analysed the relationship between individual genetic variability and two different estimators of fitness in natural samples of European eel, growth rate (using back-calculated length-at-age 1, 2 and 3) and parasite infestation by the swimbladder nematode Anguillicola crassus. Despite using a large data set of 22 expressed sequence tags-derived microsatellite loci and a large sample size of 346 individuals, no heterozygote advantage was observed in terms of growth rate or parasite load. The lack of association was evidenced by (i) nonsignificant global HFCs, (ii) a Multivariate General Linear Model showing no effect of heterozygosity on fitness components, (iii) single-locus analysis showing a lower number of significant tests than the expected false discovery rate, (iv) sign tests showing only a significant departure from expectations at one component, and, (v) a random distribution of significant single-locus HFCs that was not consistent across fitness components or sampling sites. This contrasts with the positive association observed in farmed eels in a previous study using allozymes, which can be explained by the nature of the markers used, with the allozyme study including many loci involved in metabolic energy pathways, while the expressed sequence tags-linked microsatellites might be located in genes or in the proximity of genes uncoupled with metabolism/growth.

• Genetic composition of Atlantic and Mediterranean recruits of European eel Anguilla anguilla based on EST-linked microsatellite loci.

  Authors: J M Pujolar, G A De Leo, E Ciccotti, L Zane

  Journal of fish biology. 06/2009; 74(9):2034-46.

  Anguilla anguilla glass eels arriving at two Mediterranean and two Atlantic sites were tested for differences in genetic composition between regions using a total of 23 microsatellite loci developedAnguilla anguilla glass eels arriving at two Mediterranean and two Atlantic sites were tested for differences in genetic composition between regions using a total of 23 microsatellite loci developed from an expressed sequence tag (EST) library. Hierarchical analysis of molecular variance indicated a non-significant difference between regions (Mediterranean v. Atlantic), which contrasted with the significant differences observed between samples within regions. The existence of a single spawning site for all A. anguilla individuals and extensive migration loop with great opportunity for mixing of individuals might explain the homogeneity in genetic composition found between regions. The observation of a (small-scale) pattern of genetic patchiness among intra-annual samples (arrival waves) within geographic regions does not conflict with the lack of (large-scale) geographic sub-structuring found between the Mediterranean and Atlantic regions, but most likely is a consequence of the strong dependence of A. anguilla on oceanic conditions in the Sargasso Sea that might result in a limited parental contribution to each spawning event. The comparison of Atlantic and Mediterranean A. anguilla glass eel recruits based on EST-linked microsatellite loci provides evidence supporting the hypothesis of panmixia A. anguilla across Europe.

• Polymorphic microsatellite loci in the widespread amphidromous goby Sicyopterus lagocephalus and cross-genus amplification among Sicydiinae.

  Authors: T B Hoareau, F Barbisan, S Dubois, L Zane, P Berrebi

  Molecular ecology resources. 03/2009; 9(2):607-9.

  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 withMicrosatellite 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.

• Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel (Anguilla anguilla).

  Authors: J M Pujolar, G E Maes, J K J VAN Houdt, L Zane

  Molecular ecology resources. 01/2009; 9(1):233-5.

  A European eel (Anguilla anguilla) expressed sequence tag database consisting of 795 contigs and 4008 singletons was screened for microsatellites sequences. Primers were designed to amplify 96A European eel (Anguilla anguilla) expressed sequence tag database consisting of 795 contigs and 4008 singletons was screened for microsatellites sequences. Primers were designed to amplify 96 repeats, of which 86 gave good quality amplification products. Twenty-eight microsatellites were selected for further microsatellite genotyping. Only two loci were found to be monomorphic; out of the 26 polymorphic loci, number of alleles per locus ranged from two to 14, while the observed and expected heterozygosities ranged from 0.05 to 0.93, and from 0.05 to 0.95, respectively. All 28 primer sets tested revealed positive amplification in American eel (Anguilla rostrata).

• Phylogeography of the pine processionary moth Thaumetopoea wilkinsoni in the Near East.

  Authors: M Simonato, Z Mendel, C Kerdelhué, J Rousselet, E Magnoux, P Salvato, A Roques, A. Battisti, L Zane

  Molecular ecology. 07/2007; 16(11):2273-83.

  Phylogeographic structure of the eastern pine processionary moth Thaumetopoea wilkinsoni was explored in this study by means of nested clade phylogeographic analyses of COI and COII sequences ofPhylogeographic structure of the eastern pine processionary moth Thaumetopoea wilkinsoni was explored in this study by means of nested clade phylogeographic analyses of COI and COII sequences of mitochondrial DNA and Bayesian estimates of divergence times. Intraspecific relationships were inferred and hypotheses tested to understand historical spread patterns and spatial distribution of genetic variation. Analyses revealed that all T. wilkinsoni sequences were structured in three clades, which were associated with two major biogeographic events, the colonization of the island of Cyprus and the separation of southwestern and southeastern Anatolia during the Pleistocene. Genetic variation in populations of T. wilkinsoni was also investigated using amplified fragment length polymorphisms and four microsatellite loci. Contrasting nuclear with mitochondrial data revealed recurrent gene flow between Cyprus and the mainland, related to the long-distance male dispersal. In addition, a reduction in genetic variability was observed at both mitochondrial and nuclear markers at the expanding boundary of the range, consistent with a recent origin of these populations, founded by few individuals expanding from nearby localities. In contrast, several populations fixed for one single mitochondrial haplotype showed no reduction in nuclear variability, a pattern that can be explained by recurrent male gene flow or selective sweeps at the mitochondrial level. The use of both mitochondrial and nuclear markers was essential in understanding the spread patterns and the population genetic structure of T. wilkinsoni, and is recommended to study colonizing species characterized by sex-biased dispersal.

• Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum.

  Authors: L Zane, S Marcato, L Bargelloni, E Bortolotto, C Papetti, M Simonato, V Varotto, T Patarnello

  Molecular ecology. 01/2007; 15(14):4499-511.

  The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of theThe Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.

• Nonconcordant evolutionary history of maternal and paternal lineages in Adriatic sturgeon.

  Authors: A Ludwig, L Congiu, C Pitra, J Fickel, J Gessner, F Fontana, T Patarnello, L Zane

  Molecular ecology. 01/2004; 12(12):3253-64.

  Although analyses of intraspecific variability are an important prerequisite for species identification assays, only a few studies have focused on population genetics and historical biogeography ofAlthough analyses of intraspecific variability are an important prerequisite for species identification assays, only a few studies have focused on population genetics and historical biogeography of sturgeon species. Here we present the first study on genetic variability of the last remaining Adriatic sturgeon, Acipenser naccarii, derived from mitochondrial and nuclear DNA. Our mitochondrial DNA analyses arranged individuals into three distinguished mitochondrial DNA haplogroups (Po1, Po2 and Buna). Two haplogroups (Po1 and Buna) were correlated to geographical distribution, whereas the third (Po2) was not. It was, however, very closely related to one lineage of its Ponto-Caspian sister species, A. gueldenstaedtii. The distribution of nuclear markers (microsatellites and amplified fragment length polymorphism) was strongly correlated to geographical distribution. An assignment test based on nuclear data placed no specimen of A. naccarii to A. gueldenstaedtii and vice versa. Therefore, the presence of gueldenstaedtii-like haplotypes within the Po population is either the result of a postglacial introgression or an ancestral polymorphism and does not indicate a hybrid population. The most valuable tool for forensic species identification purposes is one diagnostic deletion separating all A. naccarii from A. gueldenstaedtii. As both A. naccarii populations are genetically differentiated, stocking of sturgeon from the Po River in Italy into waters of the Buna River would jeopardize the genetic differences between both populations and should thus be avoided.

• Strategies for microsatellite isolation: a review.

  Authors: L Zane, L Bargelloni, T Patarnello

  Molecular ecology. 02/2002; 11(1):1-16.

  In the last few years microsatellites have become one of the most popular molecular markers used with applications in many different fields. High polymorphism and the relative ease of scoringIn the last few years microsatellites have become one of the most popular molecular markers used with applications in many different fields. High polymorphism and the relative ease of scoring represent the two major features that make microsatellites of large interest for many genetic studies. The major drawback of microsatellites is that they need to be isolated de novo from species that are being examined for the first time. The aim of the present paper is to review the various methods of microsatellite isolation described in the literature with the purpose of providing useful guidelines in making appropriate choices among the large number of currently available options. In addition, we propose a fast and easy protocol which is a combination of different published methods.

• Identification of interspecific hybrids by amplified fragment length polymorphism: the case of sturgeon.

  Authors: L Congiu, I Dupanloup, T Patarnello, F Fontana, R Rossi, G Arlati, L Zane

  Molecular ecology. 10/2001; 10(9):2355-9.

  The identification of interspecific hybrids represents an important issue for conservation biology and trade controls. In Italy, the commercial demand for sturgeon is rapidly increasing andThe identification of interspecific hybrids represents an important issue for conservation biology and trade controls. In Italy, the commercial demand for sturgeon is rapidly increasing and interspecific hybrids represent a relevant part of aquacultural production. In this study we tested the suitability of the amplified fragment length polymorphism (AFLP) technique for sturgeon hybrid detection. Multilocus AFLP profiles were analysed by cluster analysis and assignment tests based on observed and simulated samples. Our results show that this approach can easily identify sturgeon hybrids, encouraging its application not only in sturgeon but also in other systematic groups.

• Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography.

  Authors: L Bargelloni, S Marcato, L Zane, T Patarnello

  Systematic biology. 04/2000; 49(1):114-29.

  Antarctic waters represent a unique marine environment delimited by an oceanographic barrier, the Polar Front Zone, and characterized by constant subzero temperatures and presence of sea ice. A groupAntarctic waters represent a unique marine environment delimited by an oceanographic barrier, the Polar Front Zone, and characterized by constant subzero temperatures and presence of sea ice. A group of teleost fish, the Notothenioidei, have adapted to these challenging environmental conditions, undergoing a remarkable diversification. In the present study a total of 798 base pairs, generated from partial sequencing of 16S and 12S mitochondrial ribosomal RNA genes, were examined in 33 notothenioid species representative of all families included in the suborder Notothenioidei. Phylogenetic trees, reconstructed on the basis of sequence data by different methods, indicate that traditional hypotheses on notothenioid systematics and biogeography might be in need of reexamination. Molecular evidence suggests that vicariant speciation could be invoked to explain the early divergence of Eleginops maclovinus, a species previously included in the family Nototheniidae, which is now proposed as the closest sister group to all the rest of notothenioids apart from bovichtids. On the other hand, repeated, independent dispersal through the Polar Front is proposed for the divergence of other subantarctic notothenioid species. Likewise, multiple, independent transitions from benthic to pelagic habit are inferred from molecular data, at variance with the more conservative hypothesis based on cladograms reconstructed from morphological data.

• Novel microsatellite loci isolated from the northern krill, Meganyctiphanes norvegica (Crustacea, Euphausiacea).

  Authors: L Ostellari, L Zane, L Maccatrozzo, L Bargelloni, T Patarnello

  Molecular ecology. 04/2000; 9(3):377-8.

• Molecular evidence for genetic subdivision of Antarctic krill (Euphausia superba Dana) populations.

  Authors: L Zane, L Ostellari, L Maccatrozzo, L Bargelloni, B Battaglia, T Patarnello

  Proceedings. Biological sciences / The Royal Society. 01/1999; 265(1413):2387-91.

  Antarctic krill (Euphausia superba Dana) is a key species in the Antarctic food web and occurs on a circumcontinental scale. Population genetic structure of this species was investigated by sequenceAntarctic krill (Euphausia superba Dana) is a key species in the Antarctic food web and occurs on a circumcontinental scale. Population genetic structure of this species was investigated by sequence analysis of the ND1 mitochondrial gene in four population samples collected at different geographical localities around the Antarctic continent. Results indicate the existence of significant genetic differences between samples, and we suggest that oceanographic barriers could be sufficiently strong and temporally stable to restrict gene flow between distinct areas. Moreover, our data indicate that Antarctic krill is not at mutation-drift equilibrium and that the species possibly has a low effective population size as compared to the census size.