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Retrotransposon movements are considered to be an important factor in evolutionary processes and speciation as well as a source of genetic variation. In order to analyze genetic diversity and population structure in Tunisian pistachio species, nine inter-retrotransposon amplified polymorphism (IRAP) markers were used. As a result, eighty-six amplicons were produced among which 98.15 % were polymorphic. Mean numbers of the effective number of alleles (Ne), Shannon’s information index (I) and Nei’s genetic diversity (H) were respectively 1.529, 0.478, and 0.310. The average within-population genetic diversity (Hs) was 0.24 and the total diversity (Ht) was 0.3. The Tunisian pistachio populations exhibited high genetic differentiation (Gst =0.275) and gene flow (Nm = 1.888). The Analysis of Molecular Variance (AMOVA) indicated that variation was very high within populations (83 %). Phylogenetic tree using neighbor- joining (NJ) method and Principal Coordinates Analysis (PCoA) depicted that groupings of Tunisian varieties were made independently of the sex of the trees, but depending on their geographical origin and their breeding status. The modelbased Bayesian clustering (STRUCTURE) confirmed these observations. The inter-retrotransposons amplification polymorphism markers were significantly informative at the interspecific level. Findings reported in our study will be essential toward breeding for new pistachio genotypes with developed chemical and horticultural features.

Background The West Nile virus is a highly contagious agent for a wide range of hosts. Its spread in the Mediterranean region raises several questions about its origin and the risk factors underlying the virus’s dispersal. Materials and methods The present study aims to reconstruct the temporal and spatial phylodynamics of West Nile virus lineage 2 in the Mediterranean region using 75 complete genome sequences from different host species retrieved from international databases. Results This data set suggests that current strains of WNV-2 began spreading in South Africa or nearby regions in the early twentieth century, and it migrated northwards via at least one route crossing the Mediterranean to reach Hungary in the early 2000s, before spreading throughout Europe. Another introduction event, according to the data set collected and analyses performed, is inferred to have occurred in around 1978. Migratory birds constitute, among others, additional risk factors that enhance the geographical transmission of the infection. Conclusion Our data underline the importance of the spatial–temporal tracking of migratory birds and phylodynamic reconstruction in setting up an efficient surveillance system for emerging and reemerging zoonoses in the Mediterranean region.

This investigation aims at assessing patterns of spatial genetic structure of the teleost fish Sardina pilchardus across the Siculo-Tunisian Strait (a well-known discontinuous biogeographic area) a...

The aim of this paper was to determine how the pistachio trees evolve, and the evolving factors that influence pistachio population establishment. For that, we investigated pistachio genetic structure from some regions of Tunisia, by sequencing two noncoding chloroplastic regions (trnL (UAA) and trnL-trnF intergenic spacer). We found strong genetic diversity among groups, with the absence of high differentiation between population pairs. A deep phylogeographical break separated two major clusters: "El-Guetar and "Gafsa/Sidi-Bouzid. This conclusion is proved by the haplotype networks, the phylogenetic trees, and the molecular variance analysis. Different interpretations were proposed to explain this cytoplasm dimorphism, based on the molecular evolution and demographic history analysis: (1) the domestication events, which are very important to understand the variability between the prospective areas, (2) the gene flow between them, a process that occurs both in time and in space through pollen and seeds, and strongly interacts with the local farming systems, (3) the geographical barriers that exist, which limit gene flow transfer and make particular climatic conditions of the El-Guetar oasis. Given that, the genetic diversity study within Tunisian pistachio cultivars is very useful to contribute to the national management effort for the improvement and conservation of pistachio genetic resources. Moreover, in 2017, Tunisia ranked among the top 10 countries in global pistachio production. Thus, studying the diversity of Tunisian pistachio can make an important impact on global production.

The data presented in this paper stand as supplementary information of the associated article “Karyological characterization of the common chameleon (Chamaeleo chamaeleon) provides insights on the evolution and diversification of sex chromosomes in Chamaeleonidae” [1] . This work provides (i) raw experimental data on the karyology of the common chameleon Chamaeleo chamaeleon and (ii) the results of bioinformatic analysis on sex-specific and repeated DNA sequences found in the same species. The karyological information here presented includes traditional staining method (Giemsa staining) and sequential C-banding + fluorochromes performed on Tunisian samples of the species. The sequence data include the alignments of the isolated DNA sequences with homologous sequences found in squamate Short Read Archives (SRAs) and the results of searches in public nucleic acid databases.

The present study represents the first population structure analysis of the black sea urchin Arbacia lixula across part of its African Mediterranean distribution range, the Tunisian coast. This location is appropriate for the study of biogeographical processes given the presence of a well-known discontinuous biogeographic area (the Siculo-Tunisian Strait). Patterns of morphological and genetic variation in this highly dispersive echinoid species were assessed among its populations from the western and eastern Mediterranean coasts of Tunisia. A total of 109 specimens from six sites were collected and examined for morphometric variability in seven morphometric traits. Concordant results, inferred from CDA analyses, pairwise NPMANOVA comparisons and MDS plot, showed significant inter-population differences in the measured traits among the studied populations. In addition, UPGMA clustering and discriminant/Hotelling analysis enabled the delineation of two morphologically differentiated groups assigned to the western and eastern Mediterranean basins. SIMPER analysis showed that total dry weight and test diameter were major contributors to the morphometric separation between locations and among groups. Despite the extensive morphological variation found in A. lixula, genetic analysis of the mitochondrial COI marker recovered only a single evolutionary lineage and showed a lack of population structure as inferred from the results of one-level AMOVA and pairwise comparisons of genetic differentiation. Possible explanations for this genetic pattern are discussed. Notably, the lack of COI divergence patterns, highlighted by shallow genealogy associated with high haplotype diversity and low nucleotide diversity, together with a recent demographic expansion event retrieved from mismatch distribution and BSP analysis could be considered a residual effect of a recent evolutionary history of the species in the Mediterranean.

The present investigation focuses on population structure analysis of the purple sea urchin Paracentrotus lividus across the African Mediterranean coast, with the main aim of assessing the influence of the Siculo-Tunisian Strait on gene flow disruption in this highly dispersive echinoid species. For this purpose, patterns of morphological and genetic variation were assessed among its populations from the western and eastern Mediterranean coasts. A total of 302 specimens from seven Tunisian sites were collected and examined for morphometric variability at twelve morphometric traits. Concordant results, inferred from CDA (canonical discriminant analyses), pairwise NPMANOVA (non parametric multivariate analysis of variance) comparisons and MDS (multidimensional scaling) plot, unveiled significant inter-population differences in the measured traits among the studied populations. Furthermore, the combined use of the one way ANOSIM (analysis of similarities) and the Discriminant/Hotelling analysis allowed unravelling two morphologically differentiated groups assigned to both western and eastern Mediterranean basins. The SIMPER (similarity percentages) routine analysis showed that total dry weight, test diameter and spine length were major contributors to the morphometric separation between locations and between groups. Pattern of phenotypic divergence discerned in P. lividus across the Siculo-Tunisian Strait is interestingly in congruence with that inferred from the genetic investigation of the purple sea urchin populations from the same region based on the analysis of the mtDNA COI (cytochrome oxidase I) gene in 314 specimens from nineteen locations covering a wider geographic transect, streching westward to the Algerian coast and eastward to the Libyan littoral. The specific haplotypic composition characterizing each Mediterranean basin, as inferred from the minimum spanning network, confirmed the geographic partioning of genetic variation, as revealed by F-statistics and AMOVA (analysis of molecular variance) analyses, yielding significant genetic differentiation between eastern and western Mediterranean populations. The newly detected phylogeographic patterns, observed for the first time in P. lividus throughout the explored distribution range, suggest the involvement of different biotic and abiotic processes in shaping such variation, and provide evidence that a large and geographically exhaustive dataset is necessary to unveil phylogeographic structure within widespread marine species, previously cathegorized as panmictic in part of their distribution range.

Chameleons display high karyological diversity in chromosome number (from 2n = 20 to 62), morphology, heterochromatin distribution and location of specific chromosomal markers, making them unique study models in evolutionary cytogenetics. However, most available cytogenetic data are limited to the description of the chromosome number and morphology. Concerning sex chromosomes, our knowledge is limited to ZZ/ZW and Z1Z1Z2Z2/Z1Z2W systems in the genus Furcifer and the isolation of sex-linked, male-specific, sequences in Chamaeleo calyptratus, but the putative XY chromosomes have still to be identified in Chamaeleo and the conservation of male heterogamety in the genus needs confirmation from other species. In this study we performed a molecular and a cytogenetic analysis on C. chamaeleon, using standard, banding methods and molecular cytogenetics to provide a throughout karyological characterization of the species and to identify and locate the putative XY chromosomes. We confirm that the chromosome formula of the species is 2n = 24, with 12 metacentric macrochromosomes, 12 microchromosomes and NORs on the second chromosome pair. Heterochromatin was detected as weak C-bands on centromeric regions, differently from what was previously reported for C. calyptratus. Fluorescence in situ hybridization (FISH) showed the occurrence of interspersed telomeric signals on most macrochromosomes, suggesting that ancient chromosome fusions may have led to a reduction of the chromosome number. Using a combination of molecular and FISH analyses, we proved that male specific Restriction site-Associated DNA sequences (RADseq) isolated in C. calyptratus are conserved in C. chamaeleon and located the putative XY chromosomes on the second chromosome pair. We also identified different transposable elements in the focal taxa, which are highly interspersed on most chromosome pairs.

We investigate the influence of previously postulated biogeographic barriers in the Mediterranean Sea on the population genetic structure of a highly dispersive and continuously distributed coastal species. In particular, we examine nuclear and mitochondrial genetic variation in the marbled crab, Pachygrapsus marmoratus, across part of the African Mediterranean coast in order to assess the influence of the Siculo-Tunisian Strait on its population genetic structure. Four polymorphic microsatellite loci were genotyped for 110 individuals, collected from eight locations covering parts of the Algerian, Tunisian and Libyan coasts. In addition, mtDNA corresponding to the Cox1 gene was sequenced for 80 samples. The corresponding results show contrasting patterns of genetic differentiation. While mtDNA results revealed a homogeneous haplotype composition in our study area, microsatellite data depicted genetic differentiation among populations, but not associated with any geographic barrier. This pattern, ...

Consumers are well-informed about food additives and it is likely that they prefer natural additives over their synthetic analogues. Antioxidants represent a major class of food preservatives, among which tocopherols stand out as one of the most important examples. Interestingly, these compounds are present in relevant amounts in the mycelia of in vitro cultured mushrooms. Accordingly, the mycelia from Ganoderma lucidum, Pleurotus ostreatus and Pleurotus eryngii were used as alternative sources of tocopherols. These extracts were incorporated into different yogurt formulations, which were further compared among each other and with yogurts containing commercial α-tocopherol (E307), regarding their nutritional parameters, fatty acid profile and antioxidant activity. The proposed approach was validated as an effective functionalization strategy, particularly in the case of the G. lucidum mycelium, which showed the highest antioxidant potential, most likely as a result of its tocopherol profile. Furthermore, yogurts prepared with each mycelium extract allowed maintaining the nutritional properties observed in the “blank” yogurt formulation. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) and FEDER under Programme PT2020 for financial support to CIMO (UID/AGR/00690/2013), L. Barros and J. Barreira contracts. This work is funded by the European Regional Development Fund (ERDF) through the Regional Operational Program North 2020, within the scope of Project NORTE-01-0145-FEDER-023289: DeCodE and Project Mobilizador Norte-01-0247-FEDER-024479: ValorNatural®. info:eu-repo/semantics/publishedVersion

The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus (Fabricius, 1787) from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area (the Siculo-Tunisian Strait). Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close populations which cover almost the entire Tunisian coastline. A total of 386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyses of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA (Permutational multivariate analysis of variance). In addition, both CDA (Canonical discriminant analysis) and NPMANOVA (Non parametric MANOVA test) analyses revealed statistically significant differences among the studied locations for both sexes. Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes (North, Center and South). Specifically, SIMPER (Similarity Percentages) analysis showed that carapace length, carapace width and merus length were major contributors to the morphometric separation between populations. The pattern of phenotypic variation suggested by morphometric analyses was found to be highly discordant with that suggested by the analysis of a mitochondrial marker (cytochrome oxidase I, COI). Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity (h) were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mtDNA patterns as well as the discrepancy between them are discussed.

This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I) gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr) to 0.69 Myr (95% HPD: 0.44–0.98 Myr). This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously mentioned results.