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Diversity, Volume 6, Issue 2 (June 2014), Pages 188-395

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Research

Jump to: Review

Open AccessArticle Contrasting Patterns of Phytoplankton Assemblages in Two Coastal Ecosystems in Relation to Environmental Factors (Corsica, NW Mediterranean Sea)
Diversity 2014, 6(2), 296-322; doi:10.3390/d6020296
Received: 18 December 2013 / Revised: 18 March 2014 / Accepted: 27 March 2014 / Published: 15 April 2014
Cited by 5 | PDF Full-text (3268 KB) | HTML Full-text | XML Full-text
Abstract
Corsica Island is a sub-basin of the Northwestern Mediterranean Sea, with hydrological features typical of both oligotrophic systems and eutrophic coastal zones. Phytoplankton assemblages in two coastal ecosystems of Corsica (the deep Bay of Calvi and the shallow littoral of Bastia) show contrasting
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Corsica Island is a sub-basin of the Northwestern Mediterranean Sea, with hydrological features typical of both oligotrophic systems and eutrophic coastal zones. Phytoplankton assemblages in two coastal ecosystems of Corsica (the deep Bay of Calvi and the shallow littoral of Bastia) show contrasting patterns over a one-year cycle. In order to determine what drives these variations, seasonal changes in littoral phytoplankton are considered together with environmental parameters. Our methodology combined a survey of the physico-chemical structure of the subsurface water with a characterization of the phytoplankton community structure. Sampling provided a detailed record of the seasonal changes and successions that occur in these two areas. Results showed that the two sampled stations presented different phytoplankton abundance and distribution patterns, notably during the winter–spring bloom period. Successions in pico-, nano-, and microphytoplankton communities appeared mainly driven by differences in the ability to acquire nutrients, and in community-specific growth rates. Phytoplankton structure and dynamics are discussed in relation to available data on the Northwestern Mediterranean Sea. These results confirm that integrated monitoring of coastal areas is a requisite for gaining a proper understanding of marine ecosystems. Full article
Open AccessArticle Capacity of Aromatic Compound Degradation by Bacteria from Amazon Dark Earth
Diversity 2014, 6(2), 339-353; doi:10.3390/d6020339
Received: 10 March 2014 / Revised: 3 June 2014 / Accepted: 4 June 2014 / Published: 16 June 2014
Cited by 5 | PDF Full-text (1509 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Amazon dark earth (ADE) is known for its high organic matter content, biochar concentration and microbial diversity. The biochar amount suggests the existence of microorganisms capable of degrading aromatic hydrocarbons (AHs). In an effort to investigate the influence of bacteria on the resilience
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Amazon dark earth (ADE) is known for its high organic matter content, biochar concentration and microbial diversity. The biochar amount suggests the existence of microorganisms capable of degrading aromatic hydrocarbons (AHs). In an effort to investigate the influence of bacteria on the resilience and fertility of these soils, we enriched five ADE soils with naphthalene and phenanthrene, and biodegradation assays with phenanthrene and diesel oil were carried out, as well. After DNA extraction, amplification and sequencing of the 16S rRNA bacterial gene, we identified 148 isolates as the Proteobacteria, Firmicutes and Actinobacteria phyla comprising genera closely related to AHs biodegradation. We obtained 128 isolates that degrade diesel oil and 115 isolates that degrade phenanthrene. Some isolates were successful in degrading both substrates within 2 h. In conclusion, the obtained isolates from ADE have degrading aromatic compound activity, and perhaps, the biochar content has a high influence on this. Full article
Open AccessArticle Maintenance of Genetic Diversity in Natural Spawning of Captively-Reared Endangered Sockeye Salmon, Oncorhynchus nerka
Diversity 2014, 6(2), 354-379; doi:10.3390/d6020354
Received: 13 January 2014 / Revised: 3 June 2014 / Accepted: 3 June 2014 / Published: 19 June 2014
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Abstract
Captive propagation of Pacific salmon is routine, but few captive breeding programs have been conducted to successfully re-establish extirpated wild populations. A captive breeding program for endangered Sakinaw Lake sockeye salmon was established from 84 adults between 2002 and 2005, just prior to
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Captive propagation of Pacific salmon is routine, but few captive breeding programs have been conducted to successfully re-establish extirpated wild populations. A captive breeding program for endangered Sakinaw Lake sockeye salmon was established from 84 adults between 2002 and 2005, just prior to extirpation of the wild population. After several years of absence, sockeye salmon released from captivity returned to spawn in Sakinaw Lake in 2010 and in all years thereafter. Freshwater survival rates of released hatchery fry and naturally produced progeny of reintroduced sockeye salmon have not limited abundance of the reintroduced population. In contrast, marine survival rates for Sakinaw sockeye salmon have been <1%, a level that precludes population restoration in the absence of supplementation. Genetic diversity commensurate with the number of parental founders has been maintained in captivity. The 517 adult second-generation captive fish that spawned in Sakinaw Lake in 2011 produced a smolt emigration of almost 28,000 juvenile fish with an effective population size of 132. Allelic richness and gene diversity levels in the smolts were similar to those observed in captivity. This indicates genetic contributions from all or most founding parents have been retained both in captivity and in the nascent reintroduced natural population. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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Open AccessArticle Fish Distribution in Far Western Queensland, Australia: The Importance of Habitat, Connectivity and Natural Flows
Diversity 2014, 6(2), 380-395; doi:10.3390/d6020380
Received: 10 February 2014 / Revised: 12 June 2014 / Accepted: 18 June 2014 / Published: 24 June 2014
Cited by 1 | PDF Full-text (530 KB) | HTML Full-text | XML Full-text
Abstract
The endorheic Lake Eyre Basin drains 1.2 million square kilometres of arid central Australia, yet provides habitat for only 30 species of freshwater fish due to the scarcity of water and extreme climate. The majority are hardy riverine species that are adapted to
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The endorheic Lake Eyre Basin drains 1.2 million square kilometres of arid central Australia, yet provides habitat for only 30 species of freshwater fish due to the scarcity of water and extreme climate. The majority are hardy riverine species that are adapted to the unpredictable flow regimes, and capable of massive population booms following heavy rainfall and the restoration of connectivity between isolated waterholes. The remainder are endemic specialists from isolated springs with very restricted ranges, and many are listed under relevant state and national endangered species legislation and also by the International Union for Conservation of Nature (IUCN). For these spring communities, which are sustained by water from the Great Artesian Basin, survival is contingent on suitable habitat persisting alongside extractive mining, agriculture and the imposition of alien species. For the riverine species, which frequently undertake long migrations into ephemeral systems, preservation of the natural flow regime is paramount, as this reinstates riverine connectivity. In this study, fish were sampled from the Bulloo River in the east to the Mulligan River in the west, along a temporal timeframe and using a standard set of sampling gears. Fish presence was influenced by factors such as natural catchment divides, sampling time, ephemerality and the occurrence of connection flows and flooding. Despite the comparatively low diversity of species, the aquatic systems of this isolated region remain in good ecological condition, and as such they offer excellent opportunities to investigate the ecology of arid water systems. However, the presence of both endangered species (in the springs) and invasive and translocated species more widely indicates that active protection and management of this unique area is essential to maintain biodiversity and ecosystem integrity. Full article
(This article belongs to the Special Issue Global Freshwater Biodiversity)

Review

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Open AccessReview Diversity of Pyrrolizidine Alkaloids in the Boraginaceae Structures, Distribution, and Biological Properties
Diversity 2014, 6(2), 188-282; doi:10.3390/d6020188
Received: 6 February 2014 / Revised: 24 February 2014 / Accepted: 13 March 2014 / Published: 1 April 2014
Cited by 18 | PDF Full-text (3435 KB) | HTML Full-text | XML Full-text
Abstract
Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs) are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA
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Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs) are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA und thus cause mutations and even cancer in herbivores and humans. Almost all genera of the family Boraginaceae synthesize and store this type of alkaloids. This review reports the available information on the present status (literature up to early 2014) of the pyrrolizidine alkaloids in the Boraginaceae and summarizes the topics structure, distribution, chemistry, chemotaxonomic significance, and biological properties. Full article
Open AccessReview Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers
Diversity 2014, 6(2), 283-295; doi:10.3390/d6020283
Received: 16 February 2014 / Revised: 20 March 2014 / Accepted: 27 March 2014 / Published: 4 April 2014
Cited by 11 | PDF Full-text (486 KB) | HTML Full-text | XML Full-text
Abstract
Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of
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Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
Open AccessReview Planarian (Platyhelminthes, Tricladida) Diversity and Molecular Markers: A New View of an Old Group
Diversity 2014, 6(2), 323-338; doi:10.3390/d6020323
Received: 6 February 2014 / Revised: 24 March 2014 / Accepted: 27 March 2014 / Published: 15 April 2014
Cited by 5 | PDF Full-text (927 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many
[...] Read more.
Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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