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Diversity, Volume 5, Issue 4 (December 2013), Pages 703-855

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Research

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Open AccessArticle Molecular Identification and Historic Demography of the Marine Tucuxi (Sotalia guianensis) at the Amazon River’s Mouth by Means of Mitochondrial Control Region Gene Sequences and Implications for Conservation
Diversity 2013, 5(4), 703-723; doi:10.3390/d5040703
Received: 7 May 2013 / Revised: 9 August 2013 / Accepted: 15 August 2013 / Published: 25 September 2013
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Abstract
In 2005, three fishermen, with artisan fishing vessels and drift gillnets, accidentally captured around 200 dolphins between Vigia and Salinópolis in the Amazon River estuary. The dolphins died and they then prepared their vaginas and penises in order to sell them in the
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In 2005, three fishermen, with artisan fishing vessels and drift gillnets, accidentally captured around 200 dolphins between Vigia and Salinópolis in the Amazon River estuary. The dolphins died and they then prepared their vaginas and penises in order to sell them in the Ver-ao-Peso market in the city of Belem within the Brazilian state of Pará. We randomly sampled a minimal quantity of tissue of these sexual organs from 78 of these 200 dolphins and we determined the following results after sequencing 689 base pairs (bp) from the mitochondrial control region gene: (1) 96.15% (75/78) of these dolphins belonged to the species Sotalia guianensis. The other species detected were Steno brenadensis, Stenella coeruleoalba and Tursiops truncatus; (2) The levels of gene diversity found in this sample of S. guianensis were high (33 haplotypes, haplotype diversity of 0.917 and nucleotide diversity of 0.0045) compared to gene diversities found in other Brazilian S. guianensis locations; (3) All the population genetics methods employed indicated a clear population expansion in this population. This population expansion could have begun 400,000 years ago; (4) The haplotype divergence within this population could have begun around 2.1 millions of years ago (MYA), with posterior splits around 2.0–1.8 MYA, 1.7–1.8 MYA, 1–1.5 MYA, 0.6–0.8 MYA, 0.4–0.2 MYA and 0.16–0.02 MYA, all during the Pleistocene. Full article
(This article belongs to the Special Issue Molecular Systematic and Genetic Diversity)
Open AccessArticle Upland Habitat Quality and Historic Landscape Composition Influence Genetic Variation of a Pond-Breeding Salamander
Diversity 2013, 5(4), 724-733; doi:10.3390/d5040724
Received: 29 July 2013 / Revised: 31 August 2013 / Accepted: 10 September 2013 / Published: 25 September 2013
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Abstract
Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life
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Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life stages. One approach to management of pond-breeding species is protection of core upland habitat surrounding the breeding pond. We used genetic variation as an indicator of population status in a common amphibian species, spotted salamanders (Ambystoma maculatum), to determine how amount of suitable upland habitat relates to population status in the greater Charlotte, North Carolina, USA metropolitan area. We developed candidate models to evaluate the relative influence of historical and contemporary forested habitat availability on population genetic variation at two spatial scales of upland area (164 m and 2000 m) at four time intervals over the past seven decades (1938, 1978, 1993, 2005). We found that historical land cover best predicted contemporary allelic richness. Inbreeding coefficient and observed heterozygosity were not effectively predicted by forest cover at either spatial or temporal scales. Allelic richness was best predicted at the smaller spatial scale in the 1993 time interval. Predicting and understanding how future landscape configuration affects genetic variation of common and rare species is imperative for the conservation of amphibian and other wildlife populations. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessCommunication Oviposition Decision of the Weevil Exapion ulicis on Ulex europaeus Depends on External and Internal Pod Cues
Diversity 2013, 5(4), 734-749; doi:10.3390/d5040734
Received: 15 June 2013 / Revised: 13 August 2013 / Accepted: 13 September 2013 / Published: 30 September 2013
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Abstract
Understanding mechanisms underlying insects’ host choice and plant susceptibility is important to the study of plant-insect interactions in general, and in the context of plant invasions. This study investigates the oviposition and feeding choices of the specialist weevil Exapion ulicis on the invasive
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Understanding mechanisms underlying insects’ host choice and plant susceptibility is important to the study of plant-insect interactions in general, and in the context of plant invasions. This study investigates the oviposition and feeding choices of the specialist weevil Exapion ulicis on the invasive plant species Ulex europaeus, gorse. To do so, we studied the oviposition and feeding preferences of the weevil in choice experiments, using pods and flowers, respectively, from gorses grown in a common garden. The plants used came from regions with different infestation histories: Brittany and Scotland belong to the native range, where the weevil is present, while Reunion and New Zealand belong to the invasive range, where the weevil was not initially introduced with gorse. Results of these experiments suggest that the oviposition choice of E. ulicis females is driven by cues located at the surface of pods and inside them, including pod size and pod seed content. Feeding-choice experiments showed a different pattern of preference compared to oviposition. Taken together with previous studies, our results reveal that E. ulicis uses several traits to choose its host, including whole-plant traits, flower traits and pod traits. Full article
(This article belongs to the Special Issue Diversity of Plant-Insect Interactions)
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Open AccessArticle Novel Endophytic Trichoderma spp. Isolated from Healthy Coffea arabica Roots are Capable of Controlling Coffee Tracheomycosis
Diversity 2013, 5(4), 750-766; doi:10.3390/d5040750
Received: 28 August 2013 / Revised: 2 October 2013 / Accepted: 9 October 2013 / Published: 21 October 2013
Cited by 5 | PDF Full-text (899 KB) | HTML Full-text | XML Full-text
Abstract
One of the biggest threats to coffee growers in East Africa are emerging vascular wilt diseases (tracheomycosis) caused by Fusarium spp. Many Trichoderma species are known to be natural antagonists of these pathogens and are widely used in biological control of fungal plant
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One of the biggest threats to coffee growers in East Africa are emerging vascular wilt diseases (tracheomycosis) caused by Fusarium spp. Many Trichoderma species are known to be natural antagonists of these pathogens and are widely used in biological control of fungal plant diseases. More recently, several Trichoderma spp., which exhibited high antifungal activity have been isolated as endophytes. Consequently, we have investigated the presence and the antagonistic activity of endophytic Trichoderma isolated from roots of healthy coffee plants (Coffea arabica) from the major coffee growing regions of Ethiopia. Our results showed that community of Trichoderma spp. in roots of C. arabica contains fungi from coffee rhizosphere, as well as putatively obligate endophytic fungi. The putatively “true” endophytic species, until now, isolated only from coffee plant ecosystems in Ethiopia and recently described as T. flagellatum and novel T. sp. C.P.K. 1812 were able to antagonize Fusarium spp., which cause coffee tracheomycosis. Moreover, we found that strains of these species are also highly antagonistic against other phytopathogenic fungi, such as Alternaria alternata, Botryotinia fuckeliana (anamorph: Botrytis cinerea), and Sclerotinia sclerotiorum. Full article
Open AccessArticle Patterns of Insect Abundance and Distribution in Urban Domestic Gardens in Bangalore, India
Diversity 2013, 5(4), 767-778; doi:10.3390/d5040767
Received: 31 July 2013 / Revised: 25 September 2013 / Accepted: 14 October 2013 / Published: 22 October 2013
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Abstract
Domestic gardens may play a vital role in supporting urban insect biodiversity, despite their small size. This paper assesses the abundance, diversity and distribution of insects in urban domestic gardens in the tropics, through a study in the rapidly expanding Indian city of
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Domestic gardens may play a vital role in supporting urban insect biodiversity, despite their small size. This paper assesses the abundance, diversity and distribution of insects in urban domestic gardens in the tropics, through a study in the rapidly expanding Indian city of Bangalore. Fifty domestic gardens were studied using a combination of light traps and pitfall traps. We recorded a large number of insects, 2,185 insects from 10 orders, of which ants, bugs, beetles and flies were the most common. We found 25 species of trees (from 160 individuals) and 117 species of herbs and shrubs in the 50 sampled domestic gardens. The number of insect orders encountered was significantly related to the number of tree and herb/shrub species. Garden management practices also influenced the abundance and richness of insect orders. Thus, greater numbers of insects were observed in gardens with a greater proportion of bare soil relative to grass area and with less intensive weeding practices. More insect orders were encountered in gardens with a composting pit. Insect numbers were significantly reduced in gardens subjected to pesticide application. Most residents avoided application of pesticides and herbicides, citing health concerns. Full article
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Open AccessArticle Land and Forest Degradation inside Protected Areas in Latin America
Diversity 2013, 5(4), 779-795; doi:10.3390/d5040779
Received: 8 August 2013 / Revised: 15 October 2013 / Accepted: 5 November 2013 / Published: 13 November 2013
Cited by 8 | PDF Full-text (720 KB) | HTML Full-text | XML Full-text
Abstract
Using six years of remote sensing data, we estimated land and forest degradation inside 1788 protected areas across 19 countries in Latin America. From 2004–2009, the rate of land and forest degradation increased by 250% inside the protected areas, and the land and
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Using six years of remote sensing data, we estimated land and forest degradation inside 1788 protected areas across 19 countries in Latin America. From 2004–2009, the rate of land and forest degradation increased by 250% inside the protected areas, and the land and forest degradation totaled 1,097,618 hectares. Of the protected areas in our dataset, 45% had land and forest degradation. There were relatively large variations by major habitat type, with flooded grasslands/savannas and moist broadleaf forest protected areas having the highest rates of degradation. We found no association between a country’s rate of land and forest degradation inside protected areas and Gross Domestic Product (GDP) per capita, GDP growth, or rural population density. We found significant, but weak, associations between the rate of land and forest degradation inside protected areas and a country’s protected area system funding, the size of the protected area, and one International Union for the Conservation of Nature (IUCN) management category. Our results suggest a high degree of heterogeneity in the variables impacting land and forest degradation inside protected areas in Latin America, but that the targeting of protected area investments on a continental scale is plausible. Full article
(This article belongs to the Special Issue Biodiversity Loss & Habitat Fragmentation)
Open AccessArticle Genetic Diversity and Population Structure of Two Freshwater Copepods (Copepoda: Diaptomidae), Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan
Diversity 2013, 5(4), 796-810; doi:10.3390/d5040796
Received: 22 September 2013 / Revised: 15 November 2013 / Accepted: 18 November 2013 / Published: 22 November 2013
Cited by 2 | PDF Full-text (1241 KB) | HTML Full-text | XML Full-text
Abstract
We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four populations
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We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four populations with 51 individuals of N. schmackeri and five populations with 65 individuals of M. birulai were included. We compared the nucleotide sequences of a 635-bp fragment of the COI gene of N. schmackeri and a 655-bp fragment of the COI gene of M. birulai, and eight and 14 unique haplotypes were recorded, respectively. Tseng-Wen reservoir and Wu-San-Tao reservoir are linked by a channel, and the gene flow between them was unrestricted (Fst = 0.058; Nm = 4.04; Fst, population differentiation parameter; Nm, the number of succesfull migrants per generation); the gene flow between all other populations of both species was restricted (Fst = 0.4–0.99; Nm = 0–0.37). Based on the COI gene diversification pattern, we suggest that most populations of N. schmackeri and M. birulai are isolated from each other. According to the neighbor-joining tree and the minimum spanning network (MSN), the species have similar metapopulation genetic structures. Genetic distance was not found to be correlated with geographical distance. The genetic diversification pattern was not shown to be comparable with geographical isolation owing to long-distance separation. The genetic structure of the present populations may result from serial extinction and redistribution of the populations formed in each reservoir relative to time. Human activity in the reservoirs with regards to water resource management and the fishery industry also exerts an effect on population redistribution. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters
Diversity 2013, 5(4), 824-842; doi:10.3390/d5040824
Received: 25 September 2013 / Revised: 28 October 2013 / Accepted: 14 November 2013 / Published: 6 December 2013
Cited by 8 | PDF Full-text (1976 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Soft rot Enterobacteria in the genera Pectobacterium and Dickeya cause rotting of many crop plants. A new Dickeya isolate has been suggested to form a separate species, given the name Dickeya solani. This bacterium is spreading fast and replacing the closely related, but
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Soft rot Enterobacteria in the genera Pectobacterium and Dickeya cause rotting of many crop plants. A new Dickeya isolate has been suggested to form a separate species, given the name Dickeya solani. This bacterium is spreading fast and replacing the closely related, but less virulent, potato pathogens. The genome of D. solani isolate D s0432-1 shows highest similarity at the nucleotide level and in synteny to D. dadantii strain 3937, but it also contains three large polyketide/fatty acid/non-ribosomal peptide synthetase clusters that are not present in D. dadantii 3937. These gene clusters may be involved in the production of toxic secondary metabolites, such as oocydin and zeamine. Furthermore, the D. solani genome harbors several specific genes that are not present in other Dickeya and Pectobacterium species and that may confer advantages for adaptation to new environments. In conclusion, the fast spreading of D. solani may be related to the acquisition of new properties that affect its interaction with plants and other microbes in the potato ecosystem. Full article
(This article belongs to the Special Issue Plant-Pathogen Interactions)
Open AccessArticle Genetic Diversity and Seed Quality of the “Badda” Common Bean from Sicily (Italy)
Diversity 2013, 5(4), 843-855; doi:10.3390/d5040843
Received: 4 October 2013 / Revised: 29 November 2013 / Accepted: 2 December 2013 / Published: 6 December 2013
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Abstract
The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats
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The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats (SSR) (or microsatellite) molecular markers provided useful information on genetic variation and relationships between “Badda bianco” and “Badda nero” morphotypes. Based on SSR data, the nine accessions examined were grouped in three sub-clusters. The first sub-cluster included all the accessions belonging to the “Badda bianco”. Conversely, “Badda nero” was constituted by two well-distinguished sub-clusters, one of them forming a well-separated branch. This result suggests that two constitutive nuclei contributed to the genetic background of “Badda nero”. Moreover, technological and nutritional data evidenced a good seed protein content (mean value 240.7 g kg1) and differences in seed hydration rate among accessions. Knowledge of genetic structure appear to be fundamental in planning safeguard strategies of an appreciate landrace such as the “Badda” bean. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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Review

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Open AccessReview Patterns of Evolutionary Speed: In Search of a Causal Mechanism
Diversity 2013, 5(4), 811-823; doi:10.3390/d5040811
Received: 25 October 2013 / Revised: 21 November 2013 / Accepted: 25 November 2013 / Published: 2 December 2013
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Abstract
The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns of
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The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns of diversity and diversification. Here we review the mechanisms that have been proposed to explain these biogeographic patterns in rates of genetic evolution. Tests of several proposed mechanisms have produced equivocal results, whereas others such as those invoking annual metabolic activity, or a “Red Queen” effect, remain unexplored. However, rates of genetic evolution have been associated with both productivity mediated rates of germ cell division and active metabolic rates and these explanations therefore justify further empirical investigation. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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