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Diversity, Volume 6, Issue 1 (March 2014), Pages 1-187

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Editorial

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Open AccessEditorial Acknowledgement to Reviewers of Diversity in 2013
Diversity 2014, 6(1), 176-177; doi:10.3390/d6010176
Received: 4 March 2014 / Accepted: 4 March 2014 / Published: 4 March 2014
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Abstract The editors of Diversity would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...] Full article

Research

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Open AccessArticle Effect of Disturbance Regime on Alpha and Beta Diversity of Rock Pools
Diversity 2014, 6(1), 1-17; doi:10.3390/d6010001
Received: 5 September 2013 / Revised: 3 December 2013 / Accepted: 6 December 2013 / Published: 19 December 2013
Cited by 3 | PDF Full-text (929 KB) | HTML Full-text | XML Full-text
Abstract
Measures of alpha diversity are more frequently used to detect environmental changes and subsequent impacts on biodiversity, while measures based on variability (beta diversity) are said to be more appropriate for detecting those impacts. Theory predicts that beta diversity should increase with disturbance
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Measures of alpha diversity are more frequently used to detect environmental changes and subsequent impacts on biodiversity, while measures based on variability (beta diversity) are said to be more appropriate for detecting those impacts. Theory predicts that beta diversity should increase with disturbance frequency in patchy communities. Our objective in this study was to experimentally determine the effect of high and low disturbance regimes, frequency and intensity combined, on marine benthic alpha and beta diversity. The experiment was conducted in a rock pool system of the St. Lawrence estuary, Canada. Rock pools were disturbed by (1) nutrient enrichment and (2) draining according to three disturbance regimes (none, low, high). Disturbance regimes had little or no effect on alpha diversity of benthic algae and sessile animals. However, the low regime of nutrient enrichment induced greater within-group beta diversity than the reference rock pools, while the high disturbance regime induced equal or even smaller within-group beta diversity compared to the reference. Draining had an opposite effect on benthic beta diversity, with a greater variability of the community structure under the high regime of disturbance. Taking into account the effect of disturbance regimes on beta diversity could provide a useful diagnostic for disturbed benthic communities. Full article
Open AccessArticle Seasonal Changes in Microbial Community Structure in Freshwater Stream Sediment in a North Carolina River Basin
Diversity 2014, 6(1), 18-32; doi:10.3390/d6010018
Received: 27 October 2013 / Revised: 3 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
Cited by 4 | PDF Full-text (872 KB) | HTML Full-text | XML Full-text
Abstract
This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of
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This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of freshwater stream environments. Terminal-Restriction Fragment Length Polymorphism (T-RFLP), molecular fingerprint analysis of 16S rRNA genes was used to examine the diversity of bacterial species in stream sediment. Sediment was sampled in both wet and dry seasons from an agricultural (Bear), mixed urban (Crabtree) and forested (Marks) Creek, and the microbiota examined. Gamma, Alpha and Beta proteobacteria were prevalent species of microbial taxa represented among all sites. Actinobacteria was the next most prevalent species observed, with greater occurrence in dry compared to the wet season. Discernable clustering was observed of Marks and Bear Creek samples collected during the wetter period (September–April), which corresponded with a period of higher precipitation and cooler surface water temperatures. Although not statistically significant, microbial community structure appeared different between season (ANOSIM, R = 0.60; p < 0.10). Principal components analysis confirmed this pattern and showed that the bacterial groups were separated by wet and dry seasonal periods. These results suggest seasonal differences among the microbial community structure in sediment of freshwater streams and that these communities may respond to changes in precipitation during wetter periods. Full article
Open AccessArticle Novel Microsatellite Loci Variation and Population Genetics within Leafy Seadragons, Phycodurus eques
Diversity 2014, 6(1), 33-42; doi:10.3390/d6010033
Received: 2 October 2013 / Revised: 20 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Cited by 1 | PDF Full-text (285 KB) | HTML Full-text | XML Full-text
Abstract
Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N
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Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N = 6), Southern Australia (N = 11), and a captive group (N = 11) were analyzed. Here, we present leafy seadragon microsatellite primer sequences for all 12 loci and population genetics statistics for the six loci that amplified consistently and displayed adequate variability to estimate population parameters, such as diversity, population differences, and relatedness. Observed heterozygosities ranged from 0.225 to 0.926 and expected heterozygosities ranged from 0.278 to 0.650. Pairwise differences among populations (FST estimates) from samples collected off the southern coast of Western and South Australia, and captive animals ranged from a low of 0.188 between Southern Australia and captive animals, to a high of 0.212 between Western Australia and captive animals. Statistical assignment analyses suggested between one and three populations. Percent first order relatives among individuals was high and ranged from 40 within Western Australia to 55 within captive animals. These loci were tested on other species including weedy seadragons (Phyllopteryx taeniolatus), as well as assorted seahorses (Hippocampus reidi, H. erectus) and pipefish (Doryrhamphus dactyliophorus, D. pessuliferus, Corythoichthys intestinalis, Syngnathus leptorhynchus) with no success. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Extinction Resilience of Island Species: An Amphibian Case and a Predictive Model
Diversity 2014, 6(1), 43-71; doi:10.3390/d6010043
Received: 21 November 2013 / Revised: 4 December 2013 / Accepted: 4 December 2013 / Published: 8 January 2014
Cited by 2 | PDF Full-text (1228 KB) | HTML Full-text | XML Full-text
Abstract
Extreme overall divergence and high extinction rates are typical of insular endemics. Thus, detecting and understanding nativeness is critical on islands. Resilience to extinction is explored through a mechanistic approach focusing on midwife toads (Anura: Alytidae: Alytinae), an ancient lineage that includes continental
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Extreme overall divergence and high extinction rates are typical of insular endemics. Thus, detecting and understanding nativeness is critical on islands. Resilience to extinction is explored through a mechanistic approach focusing on midwife toads (Anura: Alytidae: Alytinae), an ancient lineage that includes continental and insular species. All alytines need urgent conservation action, including control of emerging diseases and spatially explicit reserve design aimed at ensuring ecosystem health and connectivity. The only extant insular alytine is additionally affected by an introduced continental predator. This alien species acts as a driver of the prey’s near-extinction and has not elicited any evolutionary response. Both IUCN criteria and EDGE scores show that alytines are top conservation priorities. However, there is a need for also considering phenotypic and ecological uniqueness in the assessment of conservation status and urgency. The reason is that phenotypes render ecosystems functional and insular ones uniquely so. In contrast, phylogenetic relatedness is just a constraint upon, not a motor of, evolutionary novelty. Insular species are indeed particularly susceptible, but can be similarly endangered as continental ones. This paradox may be solved by recognizing the insularity syndrome in any isolated or nearly-insular ecosystem, as a function of evolutionary and dispersal potentials. This predictive model may be useful for island biogeography, invasion biology and conservation planning. Full article
(This article belongs to the Special Issue Biogeography and Biodiversity Conservation)
Open AccessArticle Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) Marker Resources for Diversity Analysis of Mango (Mangifera indica L.)
Diversity 2014, 6(1), 72-87; doi:10.3390/d6010072
Received: 28 November 2013 / Revised: 7 January 2014 / Accepted: 7 January 2014 / Published: 20 January 2014
Cited by 6 | PDF Full-text (1073 KB) | HTML Full-text | XML Full-text
Abstract
In this study, a collection of 24,840 expressed sequence tags (ESTs) generated from five mango (Mangifera indica L.) cDNA libraries was mined for EST-based simple sequence repeat (SSR) markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST
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In this study, a collection of 24,840 expressed sequence tags (ESTs) generated from five mango (Mangifera indica L.) cDNA libraries was mined for EST-based simple sequence repeat (SSR) markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
Figures

Open AccessArticle Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism
Diversity 2014, 6(1), 88-101; doi:10.3390/d6010088
Received: 26 November 2013 / Revised: 16 January 2014 / Accepted: 17 January 2014 / Published: 24 January 2014
Cited by 8 | PDF Full-text (1271 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population
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Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP) markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC) values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ) dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA), deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
Open AccessArticle Predicting Climate Change Impacts to the Canadian Boreal Forest
Diversity 2014, 6(1), 133-157; doi:10.3390/d6010133
Received: 4 December 2013 / Revised: 19 February 2014 / Accepted: 21 February 2014 / Published: 3 March 2014
Cited by 3 | PDF Full-text (4674 KB) | HTML Full-text | XML Full-text
Abstract
Climate change is expected to alter temperature, precipitation, and seasonality with potentially acute impacts on Canada’s boreal. In this research we predicted future spatial distributions of biodiversity in Canada’s boreal for 2020, 2050, and 2080 using indirect indicators derived from remote sensing and
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Climate change is expected to alter temperature, precipitation, and seasonality with potentially acute impacts on Canada’s boreal. In this research we predicted future spatial distributions of biodiversity in Canada’s boreal for 2020, 2050, and 2080 using indirect indicators derived from remote sensing and based on vegetation productivity. Vegetation productivity indices, representing annual amounts and variability of greenness, have been shown to relate to tree and wildlife richness in Canada’s boreal. Relationships between historical satellite-derived productivity and climate data were applied to modelled scenarios of future climate to predict and map potential future vegetation productivity for 592 regions across Canada. Results indicated that the pattern of vegetation productivity will become more homogenous, particularly west of Hudson Bay. We expect climate change to impact biodiversity along north/south gradients and by 2080 vegetation distributions will be dominated by processes of seasonality in the north and a combination of cumulative greenness and minimum cover in the south. The Hudson Plains, which host the world’s largest and most contiguous wetland, are predicted to experience less seasonality and more greenness. The spatial distribution of predicted trends in vegetation productivity was emphasized over absolute values, in order to support regional biodiversity assessments and conservation planning. Full article
Open AccessCommunication Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle
Diversity 2014, 6(1), 178-187; doi:10.3390/d6010178
Received: 13 January 2014 / Revised: 26 February 2014 / Accepted: 28 February 2014 / Published: 14 March 2014
Cited by 11 | PDF Full-text (342 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of
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Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)

Review

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Open AccessReview Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran)
Diversity 2014, 6(1), 102-132; doi:10.3390/d6010102
Received: 3 December 2013 / Revised: 13 January 2014 / Accepted: 27 January 2014 / Published: 10 February 2014
Cited by 6 | PDF Full-text (1577 KB) | HTML Full-text | XML Full-text
Abstract
Urmia Lake, with a surface area between 4000 to 6000 km2, is a hypersaline lake located in northwest Iran. It is the saltiest large lake in the world that supports life. Urmia Lake National Park is the home of an almost
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Urmia Lake, with a surface area between 4000 to 6000 km2, is a hypersaline lake located in northwest Iran. It is the saltiest large lake in the world that supports life. Urmia Lake National Park is the home of an almost endemic crustacean species known as the brine shrimp, Artemia urmiana. Other forms of life include several species of algae, bacteria, microfungi, plants, birds, reptiles, amphibians and mammals. As a consequence of this unique biodiversity, this lake has been selected as one of the 59 biosphere reserves by UNESCO. This paper provides a comprehensive species checklist that needs to be updated by additional research in the future. Full article
Open AccessReview Aspects of Landscape and Pollinators—What is Important to Bee Conservation?
Diversity 2014, 6(1), 158-175; doi:10.3390/d6010158
Received: 2 December 2013 / Revised: 6 February 2014 / Accepted: 12 February 2014 / Published: 4 March 2014
Cited by 5 | PDF Full-text (560 KB) | HTML Full-text | XML Full-text
Abstract
Pollinators, especially bees, are essential to terrestrial ecosystems. They ensure the maintenance of certain ecological processes, like superior plants’ reproduction. In the past decades, agricultural intensification has caused extensive environmental changes, with major impacts on biodiversity, especially on the pollinators, which reflects the
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Pollinators, especially bees, are essential to terrestrial ecosystems. They ensure the maintenance of certain ecological processes, like superior plants’ reproduction. In the past decades, agricultural intensification has caused extensive environmental changes, with major impacts on biodiversity, especially on the pollinators, which reflects the loss of fruits and seeds sets. Here, we review studies that elucidate the causes of decline of pollinators, consequences of landscape changes to agriculture and possibilities to bees’ conservation. Many studies have related the loss of pollinators to changes in the landscape, such as the conversion of native forests into cultivated areas, which causes loss of important elements for bees (e.g., sources of pollen, nectar and oil, as well as varied nesting sites). Studies involving landscape ecology allow us to assess the effects of different farming practices over the richness and abundance of pollinators. Among the landscape elements performing positive influence on bees, the presence of remaining forests nearby cultivated areas proved to be a very important factor. Nevertheless, studies that evaluate all ground cover with a more integrated approach are still required to assess the effects of landscape context on the diversity and on the abundance of bees related to productivity of crops. Researches like these could provide specific data that strengthen the need for the conservation of different plants and animals, and could offer subsidies to propose necessary information for the execution of public and private policies, aimed at the conservation of the biodiversity. Full article
(This article belongs to the Special Issue Diversity of Plant-Insect Interactions)

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