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Diversity, Volume 2, Issue 4 (April 2010), Pages 439-700

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Research

Jump to: Review

Open AccessArticle Genetic Variability of Macedonian Tobacco Varieties Determined by Microsatellite Marker Analysis
Diversity 2010, 2(4), 439-449; doi:10.3390/d2040439
Received: 20 January 2010 / Revised: 4 February 2010 / Accepted: 2 March 2010 / Published: 24 March 2010
Cited by 4 | PDF Full-text (140 KB) | HTML Full-text | XML Full-text
Abstract
Tobacco (Nicotiana tabacum L.) is an important agricultural crop plant for the economy of many countries. Assessment of the genetic diversity of cultivated tobacco varieties is of importance for long-term tobacco improvement. Microsatellite markers are currently the marker system of choice [...] Read more.
Tobacco (Nicotiana tabacum L.) is an important agricultural crop plant for the economy of many countries. Assessment of the genetic diversity of cultivated tobacco varieties is of importance for long-term tobacco improvement. Microsatellite markers are currently the marker system of choice for genetic analysis of allopolyploid plants. In this study, we evaluated the use of 30 microsatellite markers for identification of 10 varieties of cultivated tobacco in the Republic of Macedonia. We found 24 of the microsatellite markers to be polymorphic and sufficient for identification of these varieties. Cluster analysis showed that Macedonian tobacco varieties are classifiable into three distinct groups. Full article
(This article belongs to the Special Issue Assessment of Plant Genetic Diversity)
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Open AccessArticle The Amazonian Formative: Crop Domestication and Anthropogenic Soils
Diversity 2010, 2(4), 473-504; doi:10.3390/d2040473
Received: 29 January 2010 / Revised: 12 March 2010 / Accepted: 24 March 2010 / Published: 29 March 2010
Cited by 27 | PDF Full-text (1536 KB) | HTML Full-text | XML Full-text
Abstract
The emergence of sedentism and agriculture in Amazonia continues to sit uncomfortably within accounts of South American pre-Columbian history. This is partially because deep-seated models were formulated when only ceramic evidence was known, partly because newer data continue to defy simple explanations, [...] Read more.
The emergence of sedentism and agriculture in Amazonia continues to sit uncomfortably within accounts of South American pre-Columbian history. This is partially because deep-seated models were formulated when only ceramic evidence was known, partly because newer data continue to defy simple explanations, and partially because many discussions continue to ignore evidence of pre-Columbian anthropogenic landscape transformations. This paper presents the results of recent geoarchaeological research on Amazonian anthropogenic soils. It advances the argument that properties of two different types of soils, terras pretas and terras mulatas, support their interpretation as correlates of, respectively, past settlement areas and fields where spatially-intensive, organic amendment-reliant cultivation took place. This assessment identifies anthropogenic soil formation as a hallmark of the Amazonian Formative and prompts questions about when similar forms of enrichment first appear in the Amazon basin. The paper reviews evidence for embryonic anthrosol formation to highlight its significance for understanding the domestication of a key Amazonian crop: manioc (Manihot esculenta ssp. esculenta). A model for manioc domestication that incorporates anthropogenic soils outlines some scenarios which link the distribution of its two broader varieties—sweet and bitter manioc—with the widespread appearance of Amazonian anthropogenic dark earths during the first millennium AD. Full article
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Open AccessArticle Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery
Diversity 2010, 2(4), 505-526; doi:10.3390/d2040505
Received: 13 February 2010 / Revised: 21 March 2010 / Accepted: 24 March 2010 / Published: 31 March 2010
Cited by 15 | PDF Full-text (478 KB) | HTML Full-text | XML Full-text
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 [...] 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)
Open AccessArticle The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma
Diversity 2010, 2(4), 527-549; doi:10.3390/d2040527
Received: 25 February 2010 / Revised: 24 March 2010 / Accepted: 24 March 2010 / Published: 5 April 2010
Cited by 19 | PDF Full-text (3612 KB) | HTML Full-text | XML Full-text
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 [...] 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)
Open AccessArticle Spatial Structure Alters the Shape of the Unimodal Species Richness-Biomass Relationship in a Neutral Model
Diversity 2010, 2(4), 550-560; doi:10.3390/d2040550
Received: 5 January 2010 / Revised: 30 March 2010 / Accepted: 1 April 2010 / Published: 6 April 2010
Cited by 1 | PDF Full-text (254 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Variation in individual density may explain the unimodal richness-biomass relationship in which species richness peaks at an intermediate level of total biomass. However, it is unclear how individual density is regulated by community thinning (i.e., mortality due to [...] Read more.
Variation in individual density may explain the unimodal richness-biomass relationship in which species richness peaks at an intermediate level of total biomass. However, it is unclear how individual density is regulated by community thinning (i.e., mortality due to competition with neighbors) as total above-ground biomass increases. We developed a simulation model which demonstrates that the spatial structure of a population can influence the initiation and rate of community thinning and thus the shape of the richness-biomass relationship. Specifically, we found that more clustered populations resulted in a more abrupt initiation and rapid rate of thinning and thus a sharper unimodal richness-biomass relationship. Our simulation also demonstrated that a wide diversity of richness-biomass relationships can be produced by community-thinning. Full article
(This article belongs to the Special Issue Diversity Theories and Perspectives)
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Open AccessArticle The Canarian Camel: A Traditional Dromedary Population
Diversity 2010, 2(4), 561-571; doi:10.3390/d2040561
Received: 13 January 2010 / Revised: 10 March 2010 / Accepted: 11 March 2010 / Published: 7 April 2010
Cited by 7 | PDF Full-text (500 KB) | HTML Full-text | XML Full-text
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 [...] 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)
Open AccessArticle cTBP: A Successful Intron Length Polymorphism (ILP)-Based Genotyping Method Targeted to Well Defined Experimental Needs
Diversity 2010, 2(4), 572-585; doi:10.3390/d2040572
Received: 20 February 2010 / Revised: 2 April 2010 / Accepted: 8 April 2010 / Published: 15 April 2010
Cited by 10 | PDF Full-text (1091 KB) | HTML Full-text | XML Full-text
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 [...] 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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Open AccessArticle The Diversity of Bitter Manioc (Manihot Esculenta Crantz) Cultivation in a Whitewater Amazonian Landscape
Diversity 2010, 2(4), 586-609; doi:10.3390/d2040586
Received: 23 March 2010 / Revised: 9 April 2010 / Accepted: 13 April 2010 / Published: 16 April 2010
Cited by 8 | PDF Full-text (3275 KB) | HTML Full-text | XML Full-text
Abstract
While bitter manioc has been one of the most important staple crops in the central Amazon for thousands of years, there have been few studies of its cultivation in the fertile whitewater landscapes of this region. Anthropological research on bitter manioc cultivation [...] Read more.
While bitter manioc has been one of the most important staple crops in the central Amazon for thousands of years, there have been few studies of its cultivation in the fertile whitewater landscapes of this region. Anthropological research on bitter manioc cultivation in the Amazon has focused almost exclusively on long-fallow shifting cultivation in marginal upland areas of low soil fertility. This has contributed to the persistence of the oversimplified notion that because bitter manioc is well adapted to infertile upland soils; it cannot yield well in alluvial and/or fertile soils. I hypothesized that bitter manioc cultivation would be well adapted to the fertile soils of the whitewater landscapes of the central Amazon because of the centrality of this crop to subsistence in this region. In this article, I examine one such whitewater landscape, the middle Madeira River, Amazonas, Brazil, where smallholders cultivate bitter manioc on fertile Amazonian Dark Earths (ADE) and floodplain soils, and on infertile Oxisols and Ultisols. In this region, cultivation on fertile soils tends to be short-cycled, characterised by short fallowing (0–6 years) and shorter cropping periods (5–12 months) with a predominance of low starch fast maturing “weak” landraces. By contrast, cultivation on infertile soils is normally long-cycled, characterised by longer fallows (>10 years) and longer cropping periods (1–3 years) with a predominance of high starch slow maturing “strong” landraces. This diversity in bitter manioc cultivation systems (landraces, fallow periods, soils) demonstrates that Amazonian farmers have adapted bitter manioc cultivation to the specific characteristics of the landscapes that they inhabit. I conclude that contrary to earlier claims, there are no ecological limitations on growing bitter manioc in fertile soils, and therefore the cultivation of this crop in floodplain and ADE soils would have been possible in the pre-Columbian period. Full article
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Open AccessArticle DNA Barcoding for Honey Biodiversity
Diversity 2010, 2(4), 610-617; doi:10.3390/d2040610
Received: 2 March 2010 / Revised: 8 April 2010 / Accepted: 12 April 2010 / Published: 19 April 2010
Cited by 16 | PDF Full-text (198 KB) | HTML Full-text | XML Full-text
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 [...] 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)
Open AccessArticle The Transformation of Environment into Landscape: The Historical Ecology of Monumental Earthwork Construction in the Bolivian Amazon
Diversity 2010, 2(4), 618-652; doi:10.3390/d2040619
Received: 28 January 2010 / Revised: 14 April 2010 / Accepted: 15 April 2010 / Published: 19 April 2010
Cited by 27 | PDF Full-text (2699 KB) | HTML Full-text | XML Full-text
Abstract
Although the Neotropics are recognized as a region rich in biological diversity, the origin, evolution, and maintenance of this phenomenon continues to be debated. Historical ecologists and landscape archaeologists point out that the Neotropics have a long, complex human history that may [...] Read more.
Although the Neotropics are recognized as a region rich in biological diversity, the origin, evolution, and maintenance of this phenomenon continues to be debated. Historical ecologists and landscape archaeologists point out that the Neotropics have a long, complex human history that may have been a key factor in the creation, shaping, and management of present day biodiversity. The construction of monumental earthworks referred to as ring ditches of the Bolivian Amazon and surrounding regions in late prehistory had considerable impact on the fauna, flora, soils, and topography of forest islands. Patterned landscape features, historical documents, energetics, and historical ecology are used to understand the transformation of forest islands into anthropogenic built environments. Full article
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Open AccessArticle Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata
Diversity 2010, 2(4), 653-678; doi:10.3390/d2040653
Received: 3 March 2010 / Revised: 31 March 2010 / Accepted: 13 April 2010 / Published: 22 April 2010
Cited by 4 | PDF Full-text (751 KB) | HTML Full-text | XML Full-text | Correction | Supplementary Files
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 [...] 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)

Review

Jump to: Research

Open AccessReview DNA Barcodes for Marine Biodiversity: Moving Fast Forward?
Diversity 2010, 2(4), 450-472; doi:10.3390/d2040450
Received: 1 March 2010 / Revised: 17 March 2010 / Accepted: 23 March 2010 / Published: 25 March 2010
Cited by 51 | PDF Full-text (399 KB) | HTML Full-text | XML Full-text
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 [...] 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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Open AccessReview Insights into Hemoglobin Polymorphism and Related Functional Effects on Hematological Pattern in Mediterranean Cattle, Goat and Sheep
Diversity 2010, 2(4), 679-700; doi:10.3390/d2040679
Received: 3 March 2010 / Revised: 16 April 2010 / Accepted: 19 April 2010 / Published: 22 April 2010
Cited by 7 | PDF Full-text (562 KB) | HTML Full-text | XML Full-text
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 [...] 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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