Special Issue "Biological Diversity Assessed by Molecular Methods"

Guest Editor
Dr. Lorraine Pariset
Dipartimento di Produzioni Animali, Università degli Studi della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
E-Mail:
Interests: population genetics; genetic diversity of livestock; biodiversity; molecular evolution; domestication; molecular analysis of ancient DNA; breeding strategies; genetic disorders; microarrays

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.org 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.

• genetic diversity
• polymorphism
• SNP
• microsatellite
• molecular marker
• biodiversity

Title: Phylogeographic Trends of Domestic Ruminants in Europa
Authors: D Laloë, K Moazami-Goudarzi, J.A. Lenstra
Affiliation: The European Cattle Genetic Diversity Consortium and the Econogene Consortium
Abstract: The introduction of livestock species in Europe has been followed by genetic events as introgression, selection, crossbreeding and expansion of successful breeds. This has created a complex spatial pattern of genetic differentiation. Spatial principal component analysis incorporates geographical information in an ordination analysis on allelic frequencies. This reveals axes of maximal autocovariance between geographical and genetic data as the product of a variance (diversity among populations) and a Moran index of spatial contiguity. This method was applied to four comprehensive microsatellite data sets. 101 cattle populations from Europa, Middle East and India.typed for 19 markers, 77 European cattle populations typed for 30 markers, 45 goat populations from Europa and Western Asia and 54 sheep populations from the same region typed for 31 markers. For all three species, the main genetic cline is from SouthEast to Northwest. Depending on the species, other geographical structures of genetic differentiation are revealed. Goat appears to be the most geographically structured species, with a Moran index equal to 0.92, followed by cattle (0.90) and sheep (0.86). Similar results were obtained by analyses of a genetic distance matrix. We propose this method as a useful tool to describe objectively the phylogeographic structure of a set of populations. This would allow a metaanalysis of combined datasets, since DR distances are fairly independent of the marke panel.

Type of Paper: Article
Title: Evidence of Signatures of Adaptive Evolution on the Peptide Binding Region of the Classical Chicken MHC Genes
Authors: Sheila Ommeh¹, David Lynn², Daniel Masiga³, Alessio Valentini⁴, Han Jianlin¹ and Olivier Hanotte⁵
Affiliations: ¹ International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya; E-Mail: s.ommeh@cgiar.org
²Department of Molecular Biology and Biochemistry, IRMACS Centre,Simon Fraser University, Burnaby, Vancouver B.C., Canada
³International center for Insect Physiology and Ecolology (ICIPE), P.O. Box, 30772-00100 Nairobi, Kenya
⁴Department of Animal Production, Tuscia University, Viterbo, Italy
⁵Institute of genetics, School of Biology, University of Nottingham, University Park, New Lenton, Nottingham, NG7 2RD, UK
Abstract: The BF/BL region of the classical B complex of the MHC in chicken contains candidate genes that have been associated to resistance towards several avian viral diseases. These include infectious bursal disease, lymphoid leukosis, Marek’s disease and avian influenza among others. The objective of this study was to analyse for signatures of adaptive evolution that may be present at these candidate genes. These include the BF gene that encodes the class I protein and BLA and BLB genes that encode the class II protein both of which are antigen presenting cells (APCS).
Sequences for the BF, BLA and BLB genes were obtained from the Ensembl database. Species homologs of these genes were then obtained from the NCBI BLAST and a reciprocal BLASTX was performed in order to confirm these homologs. These were then analyzed with codon models present in the PAML package for detection of signature of positive selection (dN/dS ratio).
From the results, site analysis revealed several amino acids under positive selection all of which lie in the peptide binding region (PBR). This is present in both the MHC class I protein (encoded by the BF gene) and MHC class II proteins (encoded by both the BLA and BLB genes). The PBR region in the class I molecule is encoded by alpha1 and alpha2 domains in the BF gene while the PBR region in the class II molecule is encoded by the alpha domain of the BLA gene and beta2 domain of the BLB gene. The PBR region has an important function since it is involved in antigen presentation to effector molecules.
In summary site analysis reveals that some amino acids in the PBR domains of the class I and class II molecules encoded by BF, and BLB genes are under adaptive evolution. This result is supported by samples that were sequenced in this domain and others downloaded from GenBank. They showed high diversity in the PBR region and and this warrants further research on this protein domain for its exact role towards genetic disease resistance.
Keywords: MHC; chicken; genetic resistance; dN/dS; selection

Type of Paper: Article
Title: DNA Barcoding for Honey Biodiversity
Authors: Alice Valentini, Christian Miquel and Pierre Taberlet
Affiliation: Université Grenoble 1, CNRS, UMR 5553, Laboratoire d'Ecologie Alpine, F-38041 Grenoble 09, France; E-Mail: fobemi@gmail.com (A.V.)
Abstract: Honey is produced by honeybees from nectar and from secretion of living plants. It reflects the honeybees diet and the local plant communities and it show different plant compositions in different geographical locations. We propose a new method for study the plant diversity and geographical origin of honey using a DNA barcoding approach that couples universal primers and massively parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional location and one composed by a worldwide mix of different honeys. We demonstrate that the method here proposed is suitable for study plant diversity in honey and that is fast, simple to implement, and very robust.
Keywords: DNA barcoding; trnL approach; honey; plant diversity

Title: Telomere Length Diversity in Cattle Breeds
Authors: Francesca Tilesi ¹, Lorraine Pariset ², Alessio Valentini ² and Fiorentina Ascenzioni ³
Affiliations: ¹ Department of Ecology and Sustainable Economic Development, Tuscia University, Viterbo, Italy; E-Mail: francesca.tilesi@unitus.it
² Department of Animal Production, Tuscia University, Viterbo, Italy
³ Department of Cell and Developmental Biology, “La Sapienza” University of Rome, Rome, Italy
Abstract: Telomeres are specialized nucleoprotein structures that have two important functions: i) protection of the chromosomal ends from recombinogenic events such as fusion and degradation; ii) counteracting 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 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 evidences suggest that telomeres take part to 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. In both breeds, telomere length was in the range 23-15 kb with no significant difference among the tissues. Variation among individuals within breed was very low in Chianina but rather high in Maremmana. We hypothesize that Chianina has been selected for longevity, a character which is associated with long and uniform telomeres, since many generation. This breed has a long history and its size was maintained by the Breeders Association without necessity to crossbreeding with other breeds. Maremmana was subject to the same selection, but it underwent a dramatic shrinkage of number of heads 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. As a consequence, in Maremmana we find individuals with both long (28-9 Kb) and short (22-15 Kb) telomeres which are potentially linked to different longevity characteristics.

Type of Paper: Article
Title: Application of Ecological Formulae to Studies of Molecular Evolution
Author: Joshua Drew; E-Mail: jdrew@fieldmuseum.org
Abstract: The influx of data from molecular methodologies has dramatically improved researchers’ abilities to address fundamental questions about how to best characterize the diversity of life as well as describing the processes generating that diversity. In this paper we summarize the way molecular data has helped define functional evolutionary units and introduce two methods of calculating genetic diversity structured around classical ecological formulae. We suggest that by taking a more nuanced view of measuring biodiversity we will be better able to identify key areas for conservation.

Type of Paper: Review
Title: Genome Based Approaches to the Investigation of Yeast Genetic Diversity and Population Structure
Authors: Duccio Cavalieri and Carlotta De Filippo; E-Mail: duccio.cavalieri@unifi.it
Abstract: The relationship between Yeast and Man is a passion started a few thousand years ago. The most ancient evidence for a 5158 years old Yeast driven wine fermentation was obtained from samples found in a jar from the king Scorpion tomb in Abydos (3150 bC). Despite the extensive knowledge on yeast genetics, molecular biology, genomics and biochemistry Saccharomyces cerevisiae ecological life cycle has not been yet understood, and its ecological importance is still under investigation. S. cerevisiae has been the cradle for the application of DNA based methods for analysis of biodiversity and population structure.
In this work we will discuss the several DNA fingerprinting and whole genome analysis technologies applied to study yeast evolution and variation, RAPD microsatellite analysis, sequence of selected loci and microarray based methods such as array-CGH and genotyping, and finally whole genome sequencing. We will discus the utility of the different technologies to compare the strains from different sources and collections. We will discuss how application of methods to assess yeast biodiversity by could be important in maintaining the biodiversity of products such as wine, that should include among its special attributes its yeasts.

Type of Paper: Article
Title: cTBP: A Successful ILP-Based Genotyping Method Targeted To Well Defined Experimental Needs
Author: Diego Breviario; E-Mail: terenzio@ibba.cnr.it
Abstract: There seem to be a certain degree of reluctance in accepting ILP-based methods as part of the arena of the 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 with 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.

Type of Paper: Review
Title: The Coffea Arabica Rhizosphere in Ethiopia is a Hotspot of Trichoderma Biodiversity
Authors: Temesgen M. Belayneh, Christian P. Kubicek and Irina Druzhinina; E-Mail: ckubicek@mail.zserv.tuwien.ac.at
Abstract: The African country of Ethiopia is the origin and centre of diversity of the coffee plant Coffea arabica. Today, production of coffee is severely affected by fungal wilt diseases such as Gibberella xylarioides tracheomycosis. The use of antagonistic endemic strains of Trichoderma would be a nature conserving means to combat this disease. To this end, we have investigated the Trichoderma biodiversity in the rhizosphere of C. arabica plants from farming and forest areas in four major coffee growing regions of Ethiopia. A total of 134 Isolates were identified at the species level by the oligonucleotide BarCode for Hypocrea/Trichoderma (TrichOKEY), sequence similarity analysis (TrichoBLAST) and phylogenetic inferences from elongation factor 1-alpha (tef1) sequences. 104 of the isolates comprised 8 known taxa (T. hamatum, H. lixii/T. harzianum, T. spirale, T. koningiopsis, T. atroviride, T. gamsii and T. longibrachiatum), whereas the remaining 30 isolates contained 9 putative new species. Calculation of Shannon’s H and E and Simpsons index indicated high biodiversity and lack of dominance of any species. The T. hamatum, T. asperellum and T. spirale isolates – which together made up for 55 of the 104 srains of known taxa - exhibited new tef1 alleles which formed terminal clades in Bayesian analysis indicating that these strains, respectively, form a genetically distant population within their taxon. No correlation of species occurrence of any taxon with abiotic factors was obtained. 10 randomly chosen isolates were tested for their ability to antagonize G. xylarioides growth and all were strongly positive. The new taxon T. sp. novum C.P.K. 2612 showing best results. The data show that C. arabica rhizosphere contains the highest Trichoderma biodiversity encountered so far, which is virtually not influenced by other abiotic factors. The high number of new taxa and new populations within this community suggests that C. arabica rhizosphere is a hotspot of biodiversity for Trichoderma.

Type of Paper: Article
Title: DNA Markers and FCSS Analyses Shed Light on the Genetic Diversity and Reproductive Biology of Jatropha curcas L.
Authors: Daria Ambrosi, Giulio Galla and Gianni Barcaccia
Affiliation: Laboratory of Plant Genetics and Genomics, Faculty of Agriculture, University of Padova – Campus of Agripolis, 35020 Legnaro, Padova, Italy; E-Mail: gianni.barcaccia@unipd.it
Abstract: Jatropha curcas is becoming a popular non-food oleaginous crop in several developed countries for its proposed value in the biopharmaceutical industry. Despite the potentials of its oil-rich seeds as renewable source of biodiesel and the interest towards large-scale plantation systems, basic information is scanty in this species. For instance, reproduction strategies and population dynamics are poorly understood. The extent of genetic variation within local varieties as well as the genetic differentiation between commercial varieties remains mainly uncharacterized. On the basis of available information, the vast majority of seeds should be set through sexuality, mainly by outcrossing, even though selfing could also occur. In addition, apomixis intended as asexual propagation through seeds has also been reported but not documented. Genomic DNA markers and FCSS analyses were performed to gain an insight into the population genetics and reproduction systems of Jatropha spp. The determination of ploidy and the discrimination of either pseudogamous or autonomous apomixis from sexuality were based on the seed DNA contents of embryo and endosperm. The vast majority of seeds of this species proved to include mainly diploid embryos, although a few polyploids were found. Moreover, neither 4C nor 5C endosperm DNA estimates were scored and consequently the occurrence of apomixis seems unlikely in this species. The investigation of genetic variation within and differentiation among populations was carried out exploiting dominant (RAPD, Inter-SSR, and AFLP) and codominant (SSR and SNP) markers. The main finding is that seeds commercialized worldwide are not representative of the original genepool, showing very low genetic variation either within or between varieties

Type of Paper: Article
Title: Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery
Authors: Anna V. Piterina ¹, John Barlett ² and J. Tony Pembroke ¹
Affiliations: ¹ Department of Chemical and Environmental Sciences, Material and Surface Science Institute, University of Limerick, Limerick, Ireland; E-Mail: anna.piterina@ul.ie; tony.pembroke@ul.ie
² Centre for Sustainability, Sligo Institute of Technology, Sligo, Ireland; E-Mail: bartlett.john@itsligo.ie
Abstract: Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD) was performed using a number of extraction procedures and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference of 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 rDNA libraries constructed from ATAD DNA extracted by different methods. Several modifications were necessary to optimize diversity recovery from the ATAD thermal niche which may have general applicability to diversity recovery from similar environments.
Keywords: ATAD; thermophilic sludge; DNA extraction; PCR optimisation; PCR inhibition microbial community analysis; DGGE; clone library

Type of Paper: Article
Title: Balancing selection and microsatellite variability in the critically endangered Hawaiian monk seal
Authors: Jennifer K. Schultz ^1,2, Amy J. Marshall ^3,4, Monika Pfunder ⁵
Affiliation: ¹ Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Kane'ohe, Hawai'i, United States; Email: jschultz@hawaii.edu; ² Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, Honolulu, Hawaii, United States; ³ Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand; ⁴ Department of Pathology, University of Otago, Christchurch, New Zealand; ⁵ Ecogenics GmbH, Schlieren, Switzerland
Abstract: Threatened species often exhibit low genetic diversity as a result of selection pressure, historical bottlenecks, or persistent small population size. Whereas a selective sweep creates a localized reduction of variation, a population bottleneck results in the loss of rare alleles from throughout the genome. Heterozygosity is lost more slowly than alleles and is severely impacted only when populations are small for extended periods of time. We test hypotheses of selective sweep, historical bottleneck and persistently small population size to explain the 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 112 monomorphic and 10 polymorphic loci to 35 chromosomes in the dog genome, we are able to reject the selective sweep hypothesis. Genotyping 2423 Hawaiian monk seals at the 17 polymorphic loci plus an additional locus isolated from the grey seal genome (Halichoerus grypus), we find evidence for a bottleneck (P = 0.04) consistent with historical records describing intense hunting in the 19th century. However, the bottleneck was not of sufficient duration to explain the genome-wide depletion of genetic diversity (H = 0.05; A = 1.1). Long-term small population size is a more likely explanation. Applying an FST outlier test, we find five loci to be candidates for balancing selection. Though selection is usually a weak force in small populations, it may have played a role in the preservation of minute amounts of genetic variation in the Hawaiian monk seal.

Type of Paper: Review
Title: Why Looking Back? Relevance of Ancient DNA Studies. A Review.
Authors: Ana E. Pires ¹ and Catarina Ginja ²
Affiliations: ¹ INETI - Inst. Nacional de Engenharia, Tecnologia e Inovação, Estrada do Paço do Lumiar 22,Grupo de Biologia Molecular, Edifício E 1649-038 Lisboa, Portugal; E-Mail: elisabete.pires@ineti.pt
² Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis 95616 CA, USA; E-mail: cjginja@ucdavis.edu
Abstract: In this review we summarize literature information on the relevance of ancient DNA (aDNA) studies to assess past biological diversity and infer evolutionary processes that influenced the genetic composition of present species. There is an enormous potential in the analysis of aDNA specimens, from revealing the genome of human ancestors to disentangle the origins of domesticates in relation to human migrations. We describe technical aspects of successful, authentic and reliable ancient DNA recovery, and will guide you through the interesting but complex process of analyzing DNA from archaeological remains. We will emphasize findings on aDNA studies of domestic animals to trace back domestication, infer population ranges and estimate past genetic diversity.
Keywords: ancient DNA, molecular markers, evolutionary history, archaeogenetics, forensics, domestication, paleogenomics

Type of Paper: Review
Title: DNA Barcoding for Marine Biodiversity: More Than a Trendy Approach
Authors: Adriana E. Radulovici, Philippe Archambault, Bernard Sainte-Marie, France Dufresne; Email: adriana.radulovici@uqar.qc.ca (A.E.R.)
Abstract: Biodiversity means the variety of life and 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 the patterns and processes in the marine realm, there is a need to know what species live in the oceans. DNA barcoding, based on the use of a small DNA sequence, 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.