Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families

Molecular data indicate that Rhytidhysteron rufulum (ascomycetes, Patellariales) in Costa Rica consists of four distinct lineages corroborated by morphological and chemical characters

Introduction Recent estimates of the number of fungal species worldwide predict a minimal number of over 700 K specie

Patterns of nuclear and mitochondrial DNA variation in Iberian populations of Emys orbicularis (Emydidae): conservation implications

Abstract The European pond turtle (Emys orbicularis) is threatened and in decline in several regions of its natural range, due to habitat loss combined with population fragmentation. In this work, we have focused our efforts on studying the genetic diversity and structure of Iberian populations with a fine-scale sampling (254 turtles in 10 populations) and a representation from North Africa and Balearic island populations. Using both nuclear and mitochondrial markers (seven microsatellites, *1048 bp nDNA and *1500 bp mtDNA) we have carried out phylogenetic and demographic analyses. Our results show low values of genetic diversity at the mitochondrial level although our microsatellite dataset revealed relatively high levels of genetic variability with a latitudinal genetic trend decreasing from southern to northern populations. A moderate degree of genetic differentiation was estimated for Iberian populations (genetic distances, F ST values and clusters in the Bayesian analysis). The results in this study combining mtDNA and nDNA, provide the most comprehensive population genetic data for E. orbicularis in the Iberian Peninsula. Our results suggest that Iberian populations within the Iberian-Moroccan lineage should be considered as a single subspecies with five management units, and emphasize the importance of habitat management rather than population reinforcement (i.e. captive breeding and reintroduction) in this long-lived species

Evolution of the alcohol dehydrogenase gene family in diploid and tetraploid Gossypium L

Molecular data have had a profound effect on the field of plant evolutionary biology, yet the potential wealth of data stored in low-copy nuclear-encoded genes has been virtually ignored, relative to studies of chloroplast and ribosomal DNA. In this dissertation I present an analysis of a model nuclear-encoded gene family (alcohol dehydrogenase, Adh) in a model organismal system, the cotton genus (Gossypium L., Malvaceae);A combination of PCR- and Southern hybridization-based approaches was employed to isolate, sequence, and map multiple Adh gene family members. Diploid Gossypium contain at least seven Adh loci. Sequence analysis reveals extensive intron variation between loci, and one locus has lost two introns. Evolutionary rates differ between loci and between lineages. Finally, the Adh gene family appears dynamic in that examples of gene duplication, pseudogenization, and elimination were found;We have also employed Adh genes for phylogenetic analyses. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons as a model system. We sequenced over 7 kb of CPDNA per taxon, yet obtained incomplete phylogenetic resolution. We also sequenced a 1.65-kb region of a homoeologous pair of Adh genes and obtained a robust and completely resolved topology. This enhanced resolution reflects an approximately three- to six-fold increase in evolutionary rate relative to the cpDNA sequences;Finally we have exploited Adh sequences to study intraspecific genetic diversity. We estimated nucleotide diversity for a pair of homoeologous Adh loci in allotetraploid G. hirsutum. Nucleotide diversity for AdhA in Gossypium is lower than for any plant nuclear gene yet described. This low diversity appears to reflect a history severe genetic bottlenecks supplemented by an unusually slow nucleotide substitution rate and an autogamous breeding system. While not statistically supportable, the sum of the observations also suggest differential evolutionary dynamics at each of the homoeologous loci

Bioinformatic analysis: Retroposon sequences containing multiple putative endonucleases

Among the retroposons, the source of the endonuclease activity is known to be variable. We investigated whether any retroposon genomes encode potential multiple endonuclease functions. Amino acid alignments were generated to reveal the presence of the characterized ordered-series-of-motifs (OSM) that define four different endonuclease functions. These endonuclease functions include a retroviral-like integrase (IN), an apurinic-apyrimidinic endonuclease (APE), the PDD endonuclease recently identified in the R2BM retroposon and an HNH endonuclease signature conserved by the group 11 intron sequences. The results indicate that the spliced l eader associated conserved sequences (SLACS) of T. brucei, c ruzi-associated retrotransposon (CZAR) of Trypanosoma cruzi, two crithidia retrotransposable elements (CRE); CRE1 and CRE2 of Crithidia fasciculata , and certain ING retroposon sequences of Trypanosoma brucei contain multiple putative endonuclease functions

Study of Italian isolates of Alternaria spp.: molecular and morphological characterization and pathogenesis on apple tree

It was decided to carry out a morphological and molecular characterization of the Italian Alternaria isolatescollected from apple , and evaluate their pathogenicity and subsequently combining the data collected. The strain collection (174 isolates) was constructed by collecting material (received from extension service personnel) between June and August of 2007, 2008, and 2009. A Preliminary bioassays were performed on detached plant materials (fruit and leaf wounded and unwounded), belonging to the Golden cultivar, with two different kind of inoculation (conidial suspension and conidial filtrate). Symptoms were monitored daily and a value of pathogenicity score (P.S.) was assigned on the basis of the diameter of the necrotic area that developed. On the basis of the bioassays, the number of isolates to undergo further molecular analysis was restricted to a representative set of single spore strains (44 strains). Morphological characteristics of the colony and sporulation pattern were determined according to previous systematic work on small-spored Alternaria spp. (Pryor and Michaelides, 2002 and Hong et al., 2006). Reference strains (Alternaria alternata, Alternaria tenuissima, Alternaria arborescens and four Japanese strains of Alternaria alternata mali pathotype), used in the study were kindly provided by Prof. Barry Pryor, who allows a open access to his own fungal collection. Molecular characterization was performed combining and comparing different data sets obtained from distinct molecular approach: 1) investigation of specific loci and 2) fingerprinting based on diverse randomly selected polymorphic sites of the genome. As concern the single locus analysis, it was chosen to sequence the EndoPG partial gene and three anonymous region (OPA1-3, OPA2- and OPa10-2). These markers has revealed a powerful tool in the latter systematic works on small-spored Alternaria spp. In fact, as reported in literature small-spored Alternaria taxonomy is complicated due to the inability to resolve evolutionary relationships among the taxa because of the lack of variability in the markers commonly used in fungi systematic. The three data set together provided the necessary variation to establish the phylogenetic relationships among the Italian isolates of Alternaria spp. On Italian strains these markers showed a variable number of informative sites (ranging from 7 for EndoPg to 85 for OPA1-3) and the parsimony analysis produced different tree topologies all concordant to define A. arborescens as a mophyletic clade. Fingerprinting analysis (nine ISSR primers and eight AFLP primers combination) led to the same result: a monophyleic A. arborescens clade and one clade containing both A. tenuissima and the A. alternata strains. This first attempt to characterize Italian Alternaria species recovered from apple produced concordant results with what was already described in a similar phylogenetic study on pistachio (Pryor and Michaelides, 2002), on walnut and hazelnut (Hong et al., 2006), apple (Kang et al., 2002) and citurus (Peever et al., 2004). Together with these studies, this research demonstrates that the three morphological groups are widely distributed and occupy similar ecological niches. Furthermore, this research suggest that these Alternaria species exhibit a similar infection pattern despite the taxonomic and pathogenic differences. The molecular characterization of the pathogens is a fundamental step to understanding the disease that is spreading in the apple orchards of the north Italy. At the beginning the causal agent was considered as Alteraria alternata (Marshall and Bertagnoll, 2006). Their preliminary studies purposed a pathogenic system related to the synthesis of toxins. Experimental data of our bioassays suggest an analogous hypothesis, considering that symptoms could be induced after inoculating plant material with solely the filtrate from pathogenic strains. Moreover, positive PCR reactions using AM-toxin gene specific primers, designed for identification of apple infecting Alternaria pathovar, led to a hypothesis that a host specific toxin (toxins) were involved. It remains an intriguing challenge to discover or not if the agent of the “Italian disease” is the same of the one previously typified as Alternaria mali, casual agent of the apple blotch disease

Social and population structure of striped and Risso's dolphins in the Mediterranean Sea

The aim of this research was to apply genetic methods to a better understanding of the evolution of population genetic structure in two dolphin species inhabiting a shared geographic range in the Mediterranean Sea and eastern North Atlantic (ENA). In support of this I analysed the pattern of population subdivision, genetic variability and group kin structure of striped (Stenella coeruleoalba) and Risso's dolphins (Grampus griseus) in the Mediterranean Sea, and compare theassessed the level of genetic differentiation between Mediterranean and ENA populations. The specific objectives were to: 1- study their distribution in the core study area (the Ligurian Sea) and group size variation as a possible behavioural responses to environmental features; 2- assess patterns of kinship and association within and between social groups (based on estimates of R); and 3- investigate patterns of genetic subdivision among the putative striped and Risso's dolphin populations within the Mediterranean Sea, and in comparison with the ENA. Risso's dolphins showed a clear preference for the steeper continental slope, while striped dolphins did not show this distribution preference. Samples from 165 striped dolphins were collected from the Mediterranean Sea (Adriatic, Tyrrhenian, and Spam) and ENA, and were analysed at 8 microsatellite DNA loci. The comparison between the Mediterranean and the ENA populations showed a clear separation (Fst=0.055). All loci were polymorphic (4-22 alleles), and mean Ho ranged from 0.68 in the Tyrrhenian to 0.8 in the ENA. All comparisons between putative populations showed significant differentiation, including the populations of the eastern (Adriatic) and western (Tyrrhenian) seas of Italy. Analysis of the Risso's dolphin samples (n=50) collected in the Mediterranean and the ENA showed that the two populations were significantly differentiated (Fst=0.0296). All loci were polymorphic (up to 17 alleles), and mean Ho was 0.467 m the Mediterranean, 0.548 in the ENA. Analysis of 619 bp of sequence of the mtDNA control region revealed 28 variable sites defining 16 unique haplotypes among the two populations. The degree of differentiation was highly significant for both FST (0.260) and ɸST (0.542).Individual relatedness within and between social groups of striped dolphins was investigated m the Ligurian population. On average the values were higher for intra- than inter-group comparisons, and females showed significantly higher relatedness within than between groups. The kin structure of the Risso's dolphins in the Ligurian population showed that females had a considerably higher relatedness within groups than among groups. For both species, the data suggest a relatively fluid model of kin structure with a trend for female philopatry, and male dispersal. My results indicate fine-scale population structure in both species, and significant differentiation between the Mediterranean and North Atlantic populations. A hierarchical pattern of kin structure is clearly influenced by social group structure and the dispersal behaviour of males and females, though there are some differences between the species, probably related to differences in social structure and habitat use

Molecular Population Genetics

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data