Diversity

3 pages, 174 KiB

Open AccessCorrection

Correction: Tedder, A. et al. Using chloroplast trnF pseudogenes for phylogeography in Arabidopsis lyrata. Diversity 2010, 2, 653-678

by Andrew Tedder^1,2, Peter N. Hoebe^1,3, Yvonne Willi⁴, Stephen W. Ansell⁵ and Barbara K. Mable^1,*

¹ Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow, G12 8QQ, UK

² Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland

³ Scottish Agricultural College, West Mains Road, EH9 3JG, Edinburgh, UK

⁴ Institute of Biology, Evolutionary Botany, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland

⁵ Department of Botany, The Natural History Museum, Cromwell road, London, SW7 5BD, UK

Diversity 2012, 4(1), 161-163; https://doi.org/10.3390/d4010161 - 21 Mar 2012

Viewed by 6227

Abstract

In the original version of our article [1], insufficient acknowledgement was given for the source of some of the DNA samples used. We apologize for the original error. To correct this oversight, Yvonne Willi has been added as an author, a recent paper [...] Read more.

In the original version of our article [1], insufficient acknowledgement was given for the source of some of the DNA samples used. We apologize for the original error. To correct this oversight, Yvonne Willi has been added as an author, a recent paper by Willi, Y. et al. (2010) has been added, the acknowledgements have been altered to more appropriately recognize support and funding, and the sources of samples collected have been corrected in Table 1. [...] Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

12 pages, 462 KiB

Open AccessArticle

Telomere Length Diversity in Cattle Breeds

by Francesca Tilesi^1,*,†, Enea Gino Di Domenico^2,†, Lorraine Pariset³, Luigi Bosco¹, Daniela Willems¹, Alessio Valentini³ and Fiorentina Ascenzioni²

¹ Department of Ecology and Sustainable Economic Development, Tuscia University, 01100 Viterbo, Italy

² Department of Cell and Developmental Biology, La Sapienza University of Rome, 00185 Rome, Italy

³ Department of Animal Production, Tuscia University, 01100 Viterbo, Italy

^† These authors contributed equally to this work.

Diversity 2010, 2(9), 1118-1129; https://doi.org/10.3390/d2091118 - 31 Aug 2010

Cited by 9 | Viewed by 9123

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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42 pages, 774 KiB

Open AccessReview

Methods to Estimate the Diversity in the Marine Photosynthetic Protist Community with Illustrations from Case Studies: A Review

by Linda K. Medlin^1,2,* and Wiebe H.C. F. Kooistra³

¹ UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France

² CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer, France

³ Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy

Diversity 2010, 2(7), 973-1014; https://doi.org/10.3390/d2070973 - 16 Jul 2010

Cited by 39 | Viewed by 11048

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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13 pages, 240 KiB

Open AccessReview

Using Molecular-Assisted Alpha Taxonomy to Better Understand Red Algal Biodiversity in Bermuda

by Elisabeth N. Cianciola¹, Thea R. Popolizio², Craig W. Schneider¹ and Christopher E. Lane^2,*

¹ Department of Biology, Trinity College, 300 Summit St., Hartford, CT 06106, USA

² Department of Biological Sciences, University of Rhode Island, 120 Flagg Rd., Kingston, RI 02881, USA

Diversity 2010, 2(6), 946-958; https://doi.org/10.3390/d2060946 - 17 Jun 2010

Cited by 64 | Viewed by 11191

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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14 pages, 370 KiB

Open AccessArticle

Spatial Trends of Genetic Variation of Domestic Ruminants in Europe

by Denis Laloë^1,*, Katayoun Moazami-Goudarzi¹, Johannes A. Lenstra², Paolo Ajmone Marsan³, Pedro Azor⁴, Roswitha Baumung⁵, Daniel G. Bradley⁶, Michael W. Bruford⁷, Javier Cañón⁸, Gaudenz Dolf⁹, Susana Dunner⁸, Georg Erhardt¹⁰, Godfrey Hewitt¹¹, Juha Kantanen¹², Gabriela Obexer-Ruff⁹, Ingrid Olsaker¹³, Clemen Rodellar¹⁴, Alessio Valentini¹⁵, Pamela Wiener¹⁶ and ECGDCEC^†

¹ Génétique animale et biologie intégrative, UMR 1313, Inra, 78352 Jouy-en-Josas, France

² Utrecht University, Utrecht, The Netherlands

³ Università Cattolica del S. Cuore, Piacenza, Italy

⁴ University of Córdoba, Spain

⁵ BOKU University, Vienna, Austria

⁶ Trinity College, Dublin, Ireland

⁷ University of Wales, Cardiff, UK

⁸ Universidad Complutense de Madrid, Spain

⁹ University of Berne, Switzerland

¹⁰ Justus-Liebig Universität, Giessen, Germany

¹¹ University of East Anglia, Norwich, UK

¹² MTT, Jokioinen, Finland

¹³ Norwegian School of Veterinary Science, Oslo, Norway

¹⁴ Universitat Autonoma de Barcelona, Spain

¹⁵ Università degli Studi di Milano, Italy

¹⁶ The Roslin Institute, University of Edinburgh, UK

^† The following participants of the European Cattle Genetic Diversity Consortium and the Econogene contributed to this study: P. Dobi, A. Hoda, Faculty of Agriculture, Tirana, Albania; S. Matraninon, F. Fischerleitner, BOKU University, Vienna, Austria; G. Mommens, Dr. Van Haeringen Polygen, Malle; P. Baret, A. Fadlaoui, Université Catholique, Louvain, Belgium; L.E. Holm, Danish Institute of Agricultural Sciences, Tjele, Denmark; M.A.A. El-Barody, Minia University, Egypt; P. Taberlet, G. Luikart, A. Beja-Pereira, P. England, Université Joseph Fourier et Centre National de la Recherche Scientifique, Grenoble; M. Trommetter, Université Pierre Mendes, Grenoble; A. Oulmouden, H. Levéziel, INRA, Limoges, France; O. Jann, C. Weimann, E.-M. Prinzenberg, C. Peter, Justus-Liebig Universität, Giessen; B. Harlizius, School of Veterinary Medicine, Hannover; C. Looft, E.Kalm, J. Roosen, Christian-Albrechts-Universität, Kiel, Germany; A. Georgoudis, Aristotle University, Thessaloniki; C. Ligda, National Agricultural Research Foundation, Thessaloniki, Greece; L. Fésüs, Research Institute for Animal Breeding and Nutrition, Herceghalom, Hungary; D.E. MacHugh, A.R. Freeman, Trinity College, Dublin, Ireland; R. Negrini, E. Milanesi, G. Canali, Università Cattolica del S. Cuore, Piacenza, M.C. Savarese, C. Marchitelli, L. Pariset, I. Cappuccio, Università della Tuscia, Viterbo; M. Zanotti, G. Ceriotti, M. Cicogna, P. Crepaldi, Università degli Studi di Milano; F. Pilla, A. Bruzzone, D. Iamartino, Università del Molise, Campobasso; A. Carta, T. Sechi, Istituto Zootecnico e Caseario per la Sardegna, Olmedo; G. D'Urso, S. Bordonaro, D. Marletta, Università degli Studi di Catania, Italy; M. Abo-Shehada, Jordan University of Science and Technology, Ibid, Jordan; I.J. Nijman, Utrecht University, Utrecht; M. Felius, Rotterdam, Netherlands; Norwegian School of Veterinary Science, Oslo, Norway; R. Niznikowski, Warsaw Agricultural University, Poland; A. Vlaic, University of Cluj-Napoca, Romania; T. Kiselyova, All-Russian Research Institute for Farm Animals and Breeding, St. Petersburgh-Pushkin; N. Marzanov, All-Russian Research Institute of Animal Husbandry, Dubrovitsy; Z. Ivanova, R. Popov and I. Ammosov, Yakutian Research Institute of Agricultural Sciences, Yakutsk, Sakha; M. Cinkulov, University of Novi Sad, Russia; P. Zaragoza, I. Martín-Burriel, Veterinary Faculty, Zaragoza; A. Sanchez, J. Piedrafita, Universitat Autonoma de Barcelona; E. Rodero, University of Córdoba, Spain; K. Sandberg, Swedish University of Agricultural Sciences, Uppsala, Sweden; G. Obexer-Ruff, M.-L. Glowatzki, University of Berne; R. Caloz, S. Joost, Swiss Federal Institute of Technology, Lausanne, Switzerland; O. Ertugrul, Ankara University, Ankara; I. Togan, Middle East Technical University, Ankara, Turkey; J.L. Williams, D. Burton, Roslin Institute, UK; T. Perez, University of Wales, Cardiff; S. Dalamitra, University of East Anglia, Norwich, UK.

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Diversity 2010, 2(6), 932-945; https://doi.org/10.3390/d2060932 - 17 Jun 2010

Cited by 20 | Viewed by 16825

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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18 pages, 1482 KiB

Open AccessArticle

Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal

by Jennifer K. Schultz^1,*, Amy J. Marshall^2,3 and Monika Pfunder⁴

¹ Hawai‘i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai‘i at Manoa, P.O. Box 1346; Kane‘ohe, HI 96744, USA

² Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand

³ Department of Pathology, University of Otago, Christchurch, New Zealand

⁴ ecogenics GmbH, Schlieren, Switzerland

Diversity 2010, 2(6), 863-880; https://doi.org/10.3390/d2060863 - 28 May 2010

Cited by 18 | Viewed by 10691

Abstract

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. [...] Read more.

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 (H_O = 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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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27 pages, 966 KiB

Open AccessArticle

DNA Markers and FCSS Analyses Shed Light on the Genetic Diversity and Reproductive Strategy of Jatropha curcas L.

by Daria Gigliola Ambrosi¹, Giulio Galla¹

, Marina Purelli², Tommaso Barbi², Andrea Fabbri², Sergio Lucretti³, Timothy Francis Sharbel⁴ and Gianni Barcaccia^1,*

¹ Laboratory of Plant Genetics and Genomics, College of Agriculture, University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, Padova, Italy

² Geneticlab Srl, Via Corte Ferrighi 16/B, 36025 Noventa Vicentina, Vicenza, Italy

³ ENEA, CR Casaccia, BIOTEC Section of Plant Genetics and Genomics, Via Anguillarese 301, 00123 Roma, Italy

⁴ Apomixis Research Group, Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany

Diversity 2010, 2(5), 810-836; https://doi.org/10.3390/d2050810 - 25 May 2010

Cited by 44 | Viewed by 10933

Abstract

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 [...] Read more.

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 H_e = 0.3491 and the fixation index as low as F_st = 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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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16 pages, 183 KiB

Open AccessArticle

Distinctiveness of Bean Landraces in Italy: the Case Study of the ‘Badda’ Bean

by Giulia Paniconi, Federica Gianfilippi, Pietro Mosconi and Andrea Mazzucato^*

Department of Agrobiology and Agrochemistry, Università degli Studi della Tuscia, Via S.C. de Lellis, s.n.c., 01100 Viterbo, Italy

Diversity 2010, 2(5), 701-716; https://doi.org/10.3390/d2050701 - 5 May 2010

Cited by 5 | Viewed by 8248

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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22 pages, 562 KiB

Open AccessReview

Insights into Hemoglobin Polymorphism and Related Functional Effects on Hematological Pattern in Mediterranean Cattle, Goat and Sheep

by Elisa Pieragostini^1,*, Ingrid Alloggio¹ and Ferruccio Petazzi²

¹ Department of Engineering and Management of the Agricultural, Livestock and Forest Systems, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy

² Department of Public health and Animal breeding, University of Bari, Provinciale per Casamassima, Km 3. Valenzano, 70010 Bari, Italy

Diversity 2010, 2(4), 679-700; https://doi.org/10.3390/d2040679 - 22 Apr 2010

Cited by 17 | Viewed by 13488

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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26 pages, 751 KiB

Open AccessArticle

Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata

by Andrew Tedder¹, Peter N. Hoebe¹, Stephen W. Ansell² and Barbara K. Mable^1,*

¹ Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow, G12 8QQ, UK

² Department of Botany, The Natural History Museum, Cromwell road, London, SW7 5BD, UK

Diversity 2010, 2(4), 653-678; https://doi.org/10.3390/d2040653 - 22 Apr 2010

Cited by 7 | Viewed by 9847 | Correction

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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8 pages, 198 KiB

Open AccessArticle

DNA Barcoding for Honey Biodiversity

by Alice Valentini^*, Christian Miquel and Pierre Taberlet

Université Grenoble 1, CNRS, UMR 5553, Laboratoire d'Ecologie Alpine, F-38041 Grenoble 09, France

Diversity 2010, 2(4), 610-617; https://doi.org/10.3390/d2040610 - 19 Apr 2010

Cited by 94 | Viewed by 16319

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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14 pages, 1091 KiB

Open AccessArticle

cTBP: A Successful Intron Length Polymorphism (ILP)-Based Genotyping Method Targeted to Well Defined Experimental Needs

by Luca Braglia

, Antonella Manca, Francesco Mastromauro and Diego Breviario^*

Institute of Agricultural Biology and Biotechnology (IBBA) -C.N.R Via Bassini 15, 20133 Milan, Italy

Diversity 2010, 2(4), 572-585; https://doi.org/10.3390/d2040572 - 15 Apr 2010

Cited by 31 | Viewed by 12384

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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11 pages, 500 KiB

Open AccessArticle

The Canarian Camel: A Traditional Dromedary Population

by Ursula Schulz¹, Isabel Tupac-Yupanqui², Amparo Martínez³, Susy Méndez², Juan Vicente Delgado³

, Mariano Gómez⁴, Susana Dunner² and Javier Cañón^2,*

¹ Camino del Aleman 5, 04250 Pechina, Almeria, Spain

² Laboratorio de Genética, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain

³ Laboratorio de Genética Molecular Aplicada, Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain

⁴ Servicio de Ganadería, Diputación Foral de Bizkaia, Avenida Lehendakari Agirre 9-2º, 48014 Bilbao, Spain

Diversity 2010, 2(4), 561-571; https://doi.org/10.3390/d2040561 - 7 Apr 2010

Cited by 29 | Viewed by 13617

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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23 pages, 3612 KiB

Open AccessArticle

The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma

by Temesgen Belayneh Mulaw, Christian P. Kubicek and Irina S. Druzhinina^*

Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9-1665, A-1060 Vienna, Austria

Diversity 2010, 2(4), 527-549; https://doi.org/10.3390/d2040527 - 5 Apr 2010

Cited by 56 | Viewed by 11904

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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22 pages, 478 KiB

Open AccessArticle

Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery

by Anna V. Piterina¹, John Bartlett² and J. Tony Pembroke^1,*

¹ Department of Chemical and Environmental Sciences, Material and Surface Science Institute, University of Limerick, Limerick, Ireland

² Centre for Sustainability, Institute of Technology Sligo, Sligo, Ireland

Diversity 2010, 2(4), 505-526; https://doi.org/10.3390/d2040505 - 31 Mar 2010

Cited by 34 | Viewed by 13610

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 and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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23 pages, 399 KiB

Open AccessReview

DNA Barcodes for Marine Biodiversity: Moving Fast Forward?

by Adriana E. Radulovici^1,*, Philippe Archambault² and France Dufresne¹

¹ Département de Biologie, Université du Québec à Rimouski, 300 allée des ursulines, Rimouski (QC) G5L 3A1, Canada

² Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des ursulines, Rimouski (QC) G5L 3A1, Canada

Diversity 2010, 2(4), 450-472; https://doi.org/10.3390/d2040450 - 25 Mar 2010

Cited by 156 | Viewed by 18997

Abstract

‘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 [...] Read more.

‘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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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28 pages, 400 KiB

Open AccessReview

On the Biological and Genetic Diversity in Neospora caninum

by Sarwat E. Al-Qassab¹, Michael P. Reichel^1,2 and John T. Ellis^1,*

¹ Department of Medical and Molecular Biosciences, University of Technology, Sydney, P. O. Box 123, Broadway, New South Wales 2007, Australia

² School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia 5371, Australia

Diversity 2010, 2(3), 411-438; https://doi.org/10.3390/d2030411 - 22 Mar 2010

Cited by 31 | Viewed by 15631

Abstract

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. [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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8 pages, 144 KiB

Open AccessCommunication

Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L.) as Revealed by RAPD Fingerprints

by Néjib Hasnaoui^1,2,*, Messaoud Mars¹, Jemni Chibani³ and Mokhtar Trifi²

¹ U.R. Agro-biodiversity, Higher Agronomic Institute, 4042 Chott Mariem, Sousse, Tunisia

² Laboratory of Molecular Genetics, Immunology & Biotechnology, Faculty of Sciences of Tunis, Campus University, 2092, El Manar, Tunis, Tunisia

³ Laboratory of Biochemistry & Molecular Biology, Faculty of Pharmacy, 5019 Monastir, Tunisia

Diversity 2010, 2(1), 107-114; https://doi.org/10.3390/d2010107 - 18 Jan 2010

Cited by 41 | Viewed by 10767

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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