http://www.mdpi.com/journal/diversity/special_issues/molec-methods/ Dear Colleagues, In this Diversity’s special issue we would like presenting the various methods available to assess biological diversity at the molecular level, with special consideration on innovative techniques, as of high throughput sequencing methods and high density microarrays. Also novel approaches as high-dimensional biology (the simultaneous study of “omic” sciences (including genomics for DNA variants, transcriptomics for mRNA, proteomics for proteins, and metabolomics for intermediate products of metabolism) will be taken into special account, in that they are promising as tools to address questions regarding the molecular mechanisms involved in various biological aspects, as diversity. The issue is not restrict to any particular taxa. Contributions focusing on application of molecular methods to animals, including human, and also plants, will be considered, to enrich the presentation of novel applications. Dr. Lorraine Pariset Guest Editor Related Journal Genes - an Open Access journal of genetics and genomics. Submission Information All manuscripts should be submitted to diversity@mdpi.com with a copy to the Guest Editor. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website. Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed Open Access monthly journal published by MDPI. For the first two issues, to be published in 2009 and 2010, the Article Processing Charges (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections. http://www.mdpi.com/1424-2818/2/9/1118/ Telomeres are specialized nucleoprotein structures that have two important functions: (i) protection of the chromosomal ends from deleterious events such as chromosome fusion and degradation; (ii) counteraction of the “end replication problem” by allowing telomerase-dependent or, more rarely, telomerase-independent telomere elongation. The DNA sequences underlying these activities are short simple tandem repeats, which in vertebrate consist of a variable number of TTAGGG. Telomeres dysfunction may be caused either by the absence of telomerase activity or by mutations in telomeric proteins involved in telomere length and structure regulation. Additionally, increasing experimental evidence suggests that telomeres take part in the complex network regulating cell proliferation. Accordingly, telomeres are involved in biological process such as aging and tumor progression. In this study we determined the telomere length in two bovine Italian cattle breeds, Chianina and Maremmana, which are characterized by high longevity and range breeding. In order to account for possible variation among different tissues, we have determined telomere length in different organs such as spleen, lung and liver. Overall, the median telomere length was significant lower in Chianina (11 ± 0.69 kb) than in Maremmana (12.05 ± 1.57 kb). Moreover, telomere length variation among individuals was very low in Chianina but rather high in Maremmana. These data suggest that telomere length is influenced by the breeds. This hypothesis is confirmed by the different history of these Italian breeds. Indeed, Chianina has a long history and its size was maintained by the Breeders Association without necessity to crossbreed with other breeds, whereas the population of Maremmana underwent a dramatic shrinkage in the recent past. Therefore, breeders have crossed Maremmana with other breeds, like Charolais, and have relaxed the rules for the inclusion in the herd book. http://www.mdpi.com/1424-2818/2/9/1118/ Tue, 31 Aug 2010 00:00:00 CEST Diversity 2010-08-31 2 9 Article 1118 1129 1424-2818 Telomere Length Diversity in Cattle Breeds 2010-08-31 doi: 10.3390/d2091118 Francesca Tilesi Enea Gino Di Domenico Lorraine Pariset Luigi Bosco Daniela Willems Alessio Valentini Fiorentina Ascenzioni http://www.mdpi.com/1424-2818/2/7/973/ We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has been accepted that we know less than 10% of the identified diversity in the marine microbial world and the marine micro- and pico-eukaryotes are no exception. Even the species that we think we can easily recognize are often poorly described, and even less is known of their life histories and spatial and temporal trends in their abundance and distribution. With new molecular and analytical techniques, we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. Biogeochemical reactions performed by marine photosynthetic microbial organisms constitute a major sustaining component of ecosystem functioning, and therefore, affect climate changes. New interpretations of how environmental, ecological and evolutionary processes control and structure marine ecosystem biodiversity can be made so that we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study without good analytical methods. http://www.mdpi.com/1424-2818/2/7/973/ Fri, 16 Jul 2010 00:00:00 CEST Diversity 2010-07-16 2 7 Review 973 1014 1424-2818 Methods to Estimate the Diversity in the Marine Photosynthetic Protist Community with Illustrations from Case Studies: A Review 2010-07-16 doi: 10.3390/d2070973 Medlin Kooistra http://www.mdpi.com/1424-2818/2/6/946/ Molecular-assisted alpha taxonomy has recently become an effective practice in reassessing biodiversity and floristics for a variety of different organisms. This paper presents a series of examples that have been drawn from biodiversity work being carried out on the marine red algae of Bermuda. Molecular sequencing of DNA from Bermuda samples has already begun to greatly alter the makeup of the flora as it was known just decades ago, and will help set a new database for future comparison as climate change affects species composition in the islands. http://www.mdpi.com/1424-2818/2/6/946/ Thu, 17 Jun 2010 00:00:00 CEST Diversity 2010-06-17 2 6 Review 946 958 1424-2818 Using Molecular-Assisted Alpha Taxonomy to Better Understand Red Algal Biodiversity in Bermuda 2010-06-17 doi: 10.3390/d2060946 Cianciola Popolizio Schneider Lane http://www.mdpi.com/1424-2818/2/6/932/ The introduction of livestock species in Europe has been followed by various genetic events, which created a complex spatial pattern of genetic differentiation. Spatial principal component (sPCA) analysis and spatial metric multidimensional scaling (sMDS) incorporate geography in multivariate analysis. This method was applied to three microsatellite data sets for 45 goat breeds, 46 sheep breeds, and 101 cattle breeds from Europe, Southwest Asia, and India. The first two sPCA coordinates for goat and cattle, and the first sPCA coordinate of sheep, correspond to the coordinates of ordinary PCA analysis. However, higher sPCA coordinates suggest, for all three species, additional spatial structuring. The goat is the most geographically structured species, followed by cattle. For all three species, the main genetic cline is from southeast to northwest, but other geographic patterns depend on the species. We propose sPCA and sMDS to be useful tools for describing the correlation of genetic variation with geography. http://www.mdpi.com/1424-2818/2/6/932/ Thu, 17 Jun 2010 00:00:00 CEST Diversity 2010-06-17 2 6 Article 932 945 1424-2818 Spatial Trends of Genetic Variation of Domestic Ruminants in Europe 2010-06-17 doi: 10.3390/d2060932 Denis Laloë Katayoun Moazami-Goudarzi Johannes A. Lenstra Paolo Ajmone Marsan Pedro Azor Roswitha Baumung Daniel G. Bradley Michael W. Bruford Javier Cañón Gaudenz Dolf Susana Dunner Georg Erhardt Godfrey Hewitt Juha Kantanen Gabriela Obexer-Ruff Ingrid Olsaker Clemen Rodellar Alessio Valentini Pamela Wiener European Cattle Genetic Diversity Consortium and Econogene Consortium http://www.mdpi.com/1424-2818/2/6/863/ Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the genome. Heterozygosity is lost more slowly and is severely impacted only when populations are small for an extended period of time. We test the hypotheses of selective sweep, historical bottleneck and persistently small population size to explain extremely low genetic diversity in the critically endangered Hawaiian monk seal (Monachus schauinslandi). Of 163 microsatellite loci isolated from the species’ genome, only 17 are polymorphic. Mapping 98 monomorphic and 12 polymorphic loci to 35 chromosomes throughout the dog genome, we reject the selective sweep hypothesis. Genotyping 2,423 Hawaiian monk seals at the 17 polymorphic loci plus a locus previously isolated from another pinniped species, we find evidence for a recent bottleneck (P = 0.04). This is consistent with historical records describing intense hunting in the 19th century; however, the bottleneck was not of sufficient severity and duration to explain the genome-wide depletion of genetic diversity (HO = 0.05; A = 1.1). Long-term population size restriction is a more likely explanation. Though at least two of the polymorphic loci appear to be candidates for selection, the low genetic diversity of the species may further threaten chances for survival of this critically endangered species in a changing world. http://www.mdpi.com/1424-2818/2/6/863/ Fri, 28 May 2010 00:00:00 CEST Diversity 2010-05-28 2 6 Article 863 880 1424-2818 Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal 2010-05-28 doi: 10.3390/d2060863 Schultz Marshall Pfunder http://www.mdpi.com/1424-2818/2/5/810/ Jatropha curcas L. (2n = 2x = 22) is becoming a popular non-food oleaginous crop in several developed countries due to its proposed value in the biopharmaceutical industry. Despite the potentials of its oil-rich seeds as a renewable source of biodiesel and an interest in large-scale cultivation, relatively little is known with respect to plant reproduction strategies and population dynamics. Here, genomic DNA markers and FCSS analyses were performed to gain insights into ploidy variation and heterozygosity levels of multiple accessions, and genomic relationships among commercial varieties of Jatropha grown in different geographical areas. The determination of ploidy and the differentiation of either pseudogamous or autonomous apomixis from sexuality were based on the seed DNA contents of embryo and endosperm. The presence of only a high 2C embryo peak and a smaller 3C endosperm peak (ratio 2:3) is consistent with an obligate sexual reproductive system. Because of the lack of either 4C or 5C endosperm DNA estimates, the occurrence of gametophytic apomixis seems unlikely in this species but adventitious embryony cannot be ruled out. The investigation of genetic variation within and between cultivated populations was carried out using dominant RAPD and Inter-SSR markers, and codominant SSR markers. Nei’s genetic diversity, corresponding to the expected heterozygosity, was equal to He = 0.3491 and the fixation index as low as Fst = 0.2042. The main finding is that seeds commercialized worldwide include a few closely related genotypes, which are not representative of the original Mexican gene pool, revealing high degrees of homozygosity for single varieties and very low genetic diversity between varieties. http://www.mdpi.com/1424-2818/2/5/810/ Tue, 25 May 2010 00:00:00 CEST Diversity 2010-05-25 2 5 Article 810 836 1424-2818 DNA Markers and FCSS Analyses Shed Light on the Genetic Diversity and Reproductive Strategy of Jatropha curcas L. 2010-05-25 doi: 10.3390/d2050810 Ambrosi Galla Purelli Barbi Fabbri Lucretti Sharbel Barcaccia http://www.mdpi.com/1424-2818/2/5/701/ In this study, we present the morphological and molecular characterization of the ‘Badda’ bean, a landrace of outstanding organoleptic qualities that is diffused in the area of Polizzi in the province of Palermo in Sicily, Italy. This landrace is entitled to be valorized in the local market and therefore needs a thorough description to draw criteria to establish its distinctiveness from landraces with morphological and geographical proximity. Three ‘Badda’ accessions, representing the morphological variability within the landrace, have been evaluated together with suitable references. With the help of morpho-physiological traits, digital scanning of apical leaflets and ISSR molecular markers, we describe a spectrum of descriptors useful to distinguish the ‘Badda’ accessions among themselves and from similar landraces. http://www.mdpi.com/1424-2818/2/5/701/ Wed, 05 May 2010 00:00:00 CEST Diversity 2010-05-05 2 5 Article 701 716 1424-2818 Distinctiveness of Bean Landraces in Italy: the Case Study of the ‘Badda’ Bean 2010-05-05 doi: 10.3390/d2050701 Paniconi Gianfilippi Mosconi Mazzucato http://www.mdpi.com/1424-2818/2/4/679/ This report is a review of some of the results obtained over the course of 20 years spent investigating hemoglobin phenotypes and the related functional effects on hematological patterns in ruminant breeds. Tests included qualitative and quantitative analyses of hemoglobins and qualitative and quantitative analyses of α and β globins, as well as hemochromocytometric analysis. Understanding the adaptive significance of the hemoglobin variants was the goal of most of these investigations. The advances presented in this review and the previously unpublished findings included here provide evidence that Mediterranean breeds exhibit a fair number of positively charged variants, whose possible adaptive significance is discussed. http://www.mdpi.com/1424-2818/2/4/679/ Thu, 22 Apr 2010 00:00:00 CEST Diversity 2010-04-22 2 4 Review 679 700 1424-2818 Insights into Hemoglobin Polymorphism and Related Functional Effects on Hematological Pattern in Mediterranean Cattle, Goat and Sheep 2010-04-22 doi: 10.3390/d2040679 Pieragostini Alloggio Petazzi http://www.mdpi.com/1424-2818/2/4/653/ The chloroplast trnL-F region has been extensively utilized for evolutionary analysis in plants. In the Brassicaceae this fragment contains 1–12 tandemly repeated trnF pseudogene copies in addition to the functional trnF gene. Here we assessed the potential of these highly variable, but complexly evolving duplications, to resolve the population history of the model plant Arabidopsis lyrata. While the region 5’ of the duplications had negligible sequence diversity, extensive variation in pseudogene copy number and nucleotide composition revealed otherwise cryptic population structure in eastern North America. Thus structural changes can be phylogeographically informative when pseudogene evolutionary relationships can be resolved. http://www.mdpi.com/1424-2818/2/4/653/ Thu, 22 Apr 2010 00:00:00 CEST Diversity 2010-04-22 2 4 Article 653 678 1424-2818 Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata 2010-04-22 doi: 10.3390/d2040653 Tedder Hoebe Ansell Mable http://www.mdpi.com/1424-2818/2/4/610/ Honey is produced by honeybees from nectar and from secretions of living plants. It reflects the honeybees’ diet and the local plant communities. Honey also shows different plant compositions in different geographical locations. We propose a new method for studying the plant diversity and the geographical origin of honey using a DNA barcoding approach that combines universal primers and massive parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional origin and one composed of a worldwide mix of different honeys. We demonstrate that the method proposed here is fast, simple to implement, more robust than classical methods, and therefore suitable for analyzing plant diversity in honey. http://www.mdpi.com/1424-2818/2/4/610/ Mon, 19 Apr 2010 00:00:00 CEST Diversity 2010-04-19 2 4 Article 610 617 1424-2818 DNA Barcoding for Honey Biodiversity 2010-04-19 doi: 10.3390/d2040610 Valentini Miquel Taberlet http://www.mdpi.com/1424-2818/2/4/572/ There seem to be a certain degree of reluctance in accepting ILP-based methods as part of the range of molecular markers that are classically used for plant genotyping. Indeed, since DNA polymorphism results from difference in length of fragments amplified from specific gene loci, not anonymous sequences, the number of markers that can be generated is sometime inadequate for classical phylogeny studies. Yet, ILP-based markers have many other useful advantages that should not go neglected. We support this statement by presenting a large variety of data we have been collecting for a long while regarding the use of cTBP, an ILP marker based on difference in length of the introns present within the members of the plant beta-tubulin gene family. http://www.mdpi.com/1424-2818/2/4/572/ Thu, 15 Apr 2010 00:00:00 CEST Diversity 2010-04-15 2 4 Article 572 585 1424-2818 cTBP: A Successful Intron Length Polymorphism (ILP)-Based Genotyping Method Targeted to Well Defined Experimental Needs 2010-04-15 doi: 10.3390/d2040572 Braglia Manca Mastromauro Breviario http://www.mdpi.com/1424-2818/2/4/561/ The domestic camel (dromedary) is the most important livestock species in the Canary Islands and the most important autochthonous European camel population. After six centuries of a successful adaptation process to the particular environment of the Canary Islands, the abandonment of traditional agriculture has led this population to a major bottleneck. Along with a lack of foreign genetic interchanges, this could lead the population to the brink of extinction. Genetic analysis using 13 microsatellites showed the closest genetic proximity to the North African (Tindouf, Algeria) camel population and a certain degree of sub-division, with significant genetic differences among breeders. An important level of genetic differentiation among the different populations analyzed was found with a global FST value of 0.116. http://www.mdpi.com/1424-2818/2/4/561/ Wed, 07 Apr 2010 00:00:00 CEST Diversity 2010-04-07 2 4 Article 561 571 1424-2818 The Canarian Camel: A Traditional Dromedary Population 2010-04-07 doi: 10.3390/d2040561 Schulz Tupac-Yupanqui Martínez Méndez Delgado Gómez Dunner Cañón http://www.mdpi.com/1424-2818/2/4/527/ The southwestern highlands forests of Ethiopia are the origin of the coffee plant Coffea arabica. The production of coffee in this area is affected by tracheomycosis caused by a soil-born fungus Gibberella xylarioides. The use of endemic antagonistic strains of mycoparasitic Trichoderma species would be a nature conserving means to combat this disease. We have used molecular methods to reveal that the community of Trichoderma in the rhizosphere of C. arabica in its native forests is highly diverse and includes many putatively endemic species. Among others, the putative new species were particularly efficient to inhibit growth of G. xylarioides. http://www.mdpi.com/1424-2818/2/4/527/ Mon, 05 Apr 2010 00:00:00 CEST Diversity 2010-04-05 2 4 Article 527 549 1424-2818 The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma 2010-04-05 doi: 10.3390/d2040527 Belayneh Mulaw Kubicek Druzhinina http://www.mdpi.com/1424-2818/2/4/505/ Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD), was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sludge. Addition of selected adjuvant restored the ability to amplify community DNA, derived from the thermophilic sludge, via a number of primer sets of ecological importance and various DNA polymerases. Resolution of community profiles by molecular techniques was also influenced by the ATAD sludge extraction procedure as demonstrated by PCR-DGGE profiling and comparison of taxonomic affiliations of the most predominant members within 16S rRNA gene libraries constructed from ATAD DNA extracted by different methods. Several modifications have been shown to be necessary to optimize the molecular analysis of the ATAD thermal niche which may have general applicability to diversity recovery from similar environments. http://www.mdpi.com/1424-2818/2/4/505/ Wed, 31 Mar 2010 00:00:00 CEST Diversity 2010-03-31 2 4 Article 505 526 1424-2818 Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery 2010-03-31 doi: 10.3390/d2040505 Piterina Bartlett Pembroke http://www.mdpi.com/1424-2818/2/4/450/ ‘Biodiversity’ means the variety of life and it can be studied at different levels (genetic, species, ecosystem) and scales (spatial and temporal). Last decades showed that marine biodiversity has been severely underestimated at all levels. In order to investigate diversity patterns and underlying processes, there is a need to know what species live in the marine environment. An emerging tool for species identification, DNA barcoding can reliably assign unknown specimens to known species, also flagging potential cryptic species and genetically distant populations. This paper will review the role of DNA barcoding for the study of marine biodiversity at the species level. http://www.mdpi.com/1424-2818/2/4/450/ Thu, 25 Mar 2010 00:00:00 CET Diversity 2010-03-25 2 4 Review 450 472 1424-2818 DNA Barcodes for Marine Biodiversity: Moving Fast Forward? 2010-03-25 doi: 10.3390/d2040450 Radulovici Archambault Dufresne http://www.mdpi.com/1424-2818/2/3/411/ Neospora caninum is a parasite regarded a major cause of foetal loss in cattle. A key requirement to an understanding of the epidemiology and pathogenicity of N. caninum is knowledge of the biological characteristics of the species and the genetic diversity within it. Due to the broad intermediate host range of the species, worldwide geographical distribution and its capacity for sexual reproduction, significant biological and genetic differences might be expected to exist. N. caninum has now been isolated from a variety of different host species including dogs and cattle. Although isolates of this parasite show only minor differences in ultrastructure, considerable differences have been reported in pathogenicity using mainly mouse models. At the DNA level, marked levels of polymorphism between isolates were detected in mini- and microsatellites found in the genome of N. caninum. Knowledge of what drives the biological differences that have been observed between the various isolates at the molecular level is crucial in aiding our understanding of the epidemiology of this parasite and, in turn, the development of efficacious strategies, such as live vaccines, for controlling its impact. The purpose of this review is to document and discuss for the first time, the nature of the diversity found within the species Neospora caninum. http://www.mdpi.com/1424-2818/2/3/411/ Mon, 22 Mar 2010 00:00:00 CET Diversity 2010-03-22 2 3 Review 411 438 1424-2818 On the Biological and Genetic Diversity in Neospora caninum 2010-03-22 doi: 10.3390/d2030411 Al-Qassab Reichel Ellis http://www.mdpi.com/1424-2818/2/1/107/ The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD) method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop. http://www.mdpi.com/1424-2818/2/1/107/ Mon, 18 Jan 2010 00:00:00 CET Diversity 2010-01-18 2 1 Communication 107 114 1424-2818 Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L.) as Revealed by RAPD Fingerprints 2010-01-18 doi: 10.3390/d2010107 Néjib Hasnaoui Messaoud Mars Jemni Chibani Mokhtar Trifi