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Diversity, Volume 11, Issue 12 (December 2019) – 28 articles

Cover Story (view full-size image): Underground ecosystems are one of the most inhospitable places for microorganism development. Therefore, any organic matter located in these areas can stimulate fungal growth. Our research object is evidence of these observations. Paleolithic bones of cave bear (Ursus spelaeus) were exhibited for tourists in the Niedźwiedzia Cave, and mycelium growth was visible on their surface. Our studies allowed us to identify fungal species colonizing the bones and to determine susceptibility profiles to three commercially available fungicidal preparations. We also prepared recommendations that allowed us to resolve a pressing problem and effectively preserve priceless museum objects for the future. View this paper
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Open AccessArticle
Conservation Status and Challenges of the Atlantic Forest Birds of Paraguay
Diversity 2019, 11(12), 247; https://doi.org/10.3390/d11120247 - 17 Dec 2019
Viewed by 1240
Abstract
The Atlantic Forest, one of the most biodiverse biomes in the world, is also one of the most endangered. In Paraguay, its remnants are mostly fragmented and isolated. The Paraguay Biodiversity Corridor is an initiative that is being developed to generate and maintain [...] Read more.
The Atlantic Forest, one of the most biodiverse biomes in the world, is also one of the most endangered. In Paraguay, its remnants are mostly fragmented and isolated. The Paraguay Biodiversity Corridor is an initiative that is being developed to generate and maintain connectivity of the main conservation areas. With the objective to analyze the bird richness and occurrence in each of the core areas of this corridor, we gathered published data, details of the management plans, and bird surveys recorded during 2015 and 2017 in these areas. In total, 557 bird species occur in the core areas of the Corridor, representing more than 80% of the birds of the country. San Rafael National Park and Mbaracayú Forest Nature Reserve are the richest areas, with 427 (70) and 408 (61) bird species (Atlantic forest endemics), respectively. These two areas also harbor more than 30 bird species of global conservation concern. Only 24% of the Corridor area is protected or sustainably managed, with only 10% under strict protection. The Corridor situated within this endangered biome encompasses some of the most important areas for bird conservation, but the situation of many of these areas is alarming as they are not protected or effectively managed to conserve their biodiversity. Restoration of connectivity, legal enforcement, and strengthening of authorities to combat deforestation on core areas, along with research focused on the impact contributed by human activities (selective logging, ecotoxicity exposure to agrochemicals) are key actions prioritized for the Upper Parana Atlantic forest (UPAF) Corridor. Full article
(This article belongs to the Section Animal Diversity)
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Open AccessArticle
Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense
Diversity 2019, 11(12), 246; https://doi.org/10.3390/d11120246 - 17 Dec 2019
Cited by 5 | Viewed by 795
Abstract
This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils [...] Read more.
This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species. Full article
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Open AccessReview
The Patagonian Sheepdog: Historical Perspective on a Herding Dog in Chile
Diversity 2019, 11(12), 245; https://doi.org/10.3390/d11120245 - 17 Dec 2019
Cited by 1 | Viewed by 1225
Abstract
The “Patagonian Sheepdog” is a local working dog breed that was produced by selection from European working sheepdogs that arrived in the Magallanes region of southern Chile in the late nineteenth and early twentieth centuries. Currently, the Patagonian Sheepdog is most commonly found [...] Read more.
The “Patagonian Sheepdog” is a local working dog breed that was produced by selection from European working sheepdogs that arrived in the Magallanes region of southern Chile in the late nineteenth and early twentieth centuries. Currently, the Patagonian Sheepdog is most commonly found in the Chilean Patagonian region (43°12’ S to 56°30’ S), where it plays a fundamental role as a working dog in sheep and, to some extent, in cattle farming. Dog types that may have contributed to the Patagonian Sheepdog include the Old Welsh Grey and other old UK herding dogs. The modern Patagonian Sheepdog has been selectively bred by local sheep farmers to produce a herding dog that is well adapted to the area: a medium body size, long or semi-long fur, drooping or semi-erect ears, a docile character, and a great aptitude for sheep herding. Morphological studies have determined the body measurements, zoometric indices, coat color, and marking for Patagonian Sheepdogs. The objective of this investigation was to collect historical information related to the presence of this dog in Chilean Patagonia, providing general aspects of the morphology and behavior, all key factors for the recognition and conservation of this little-known herding dog. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessArticle
Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking
Diversity 2019, 11(12), 244; https://doi.org/10.3390/d11120244 - 17 Dec 2019
Cited by 1 | Viewed by 749
Abstract
A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic [...] Read more.
A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic conservation and security for the U.S. livestock sector. Samples in the collection span 60 years, suggesting a wide range of genetic diversity and genetic change is represented for rare and major breeds. Classifying breeds into four groups based upon registration or census estimates of population size of < 1000, < 5000, < 20,000, and > 20,000 indicated that 50% of the collection is comprised of rare breeds in the < 1000 category. As anticipated, collections for breeds in the < 20,000 and > 20,000 are more complete (86% and 98%, respectively) based upon an index combining the number of germplasm samples and the number of animals. For the rarest breeds (< 1000), collection completeness was 45%. Samples from over 6000 animals in the collection have been used for adding diversity to breeds, genomic evaluation, reconstituting populations, or various research projects. Several aspects of collecting germplasm samples from rare breeds are discussed. In addition, approaches that could be used to enhance the status of rare breeds via the repository use are presented. However, given the array of obstacles confronting rare breeds, the gene bank may be the most secure prospect for the long-term conservation of rare breed genetics. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessReview
Diagnosis of Varroa Mite (Varroa destructor) and Sustainable Control in Honey Bee (Apis mellifera) Colonies—A Review
Diversity 2019, 11(12), 243; https://doi.org/10.3390/d11120243 - 16 Dec 2019
Cited by 3 | Viewed by 1280
Abstract
Determining varroa mite infestation levels in honey bee colonies and the proper method and time to perform a diagnosis are important for efficient mite control. Performing a powdered sugar shake or counting mites that drop from combs and bees onto a hive bottom [...] Read more.
Determining varroa mite infestation levels in honey bee colonies and the proper method and time to perform a diagnosis are important for efficient mite control. Performing a powdered sugar shake or counting mites that drop from combs and bees onto a hive bottom board are two reliable methods for sampling varroa mite to evaluate the efficacy of an acaricide treatment. This overview summarizes studies that examine the efficacy of organic acids and essential oils, mite monitoring, and brood interruption for integrated varroa mite control in organic beekeeping. Full article
(This article belongs to the Special Issue Monitoring of Honey Bee Colony Losses)
Open AccessArticle
Diatoms Dominate and Alter Marine Food-Webs When CO2 Rises
Diversity 2019, 11(12), 242; https://doi.org/10.3390/d11120242 - 16 Dec 2019
Cited by 9 | Viewed by 1221
Abstract
Diatoms are so important in ocean food-webs that any human induced changes in their abundance could have major effects on the ecology of our seas. The large chain-forming diatom Biddulphia biddulphiana greatly increases in abundance as pCO2 increases along natural seawater [...] Read more.
Diatoms are so important in ocean food-webs that any human induced changes in their abundance could have major effects on the ecology of our seas. The large chain-forming diatom Biddulphia biddulphiana greatly increases in abundance as pCO2 increases along natural seawater CO2 gradients in the north Pacific Ocean. In areas with reference levels of pCO2, it was hard to find, but as seawater carbon dioxide levels rose, it replaced seaweeds and became the main habitat-forming species on the seabed. This diatom algal turf supported a marine invertebrate community that was much less diverse and completely differed from the benthic communities found at present-day levels of pCO2. Seawater CO2 enrichment stimulated the growth and photosynthetic efficiency of benthic diatoms, but reduced the abundance of calcified grazers such as gastropods and sea urchins. These observations suggest that ocean acidification will shift photic zone community composition so that coastal food-web structure and ecosystem function are homogenised, simplified, and more strongly affected by seasonal algal blooms. Full article
(This article belongs to the Special Issue The Effects of Ocean Acidification on Marine Phytoplankton)
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Open AccessArticle
Continuous Agrochemical Treatments in Agroecosystems Can Modify the Effects of Pendimethalin-Based Herbicide Exposure on Immunocompetence of a Beneficial Ground Beetle
Diversity 2019, 11(12), 241; https://doi.org/10.3390/d11120241 - 16 Dec 2019
Cited by 1 | Viewed by 683
Abstract
Herbicide application for pest control can negatively affect soil biodiversity, mainly acting on species that are involved in ecosystem service. In this study, field and laboratory trials were designed to assay herbicide exposure effects on the constitutive immunity of Harpalus (Pseudoophonus) rufipes (De [...] Read more.
Herbicide application for pest control can negatively affect soil biodiversity, mainly acting on species that are involved in ecosystem service. In this study, field and laboratory trials were designed to assay herbicide exposure effects on the constitutive immunity of Harpalus (Pseudoophonus) rufipes (De Geer, 1774), a beneficial carabid species that inhabits croplands. The circulating hemocytes (THCs) and plasmatic levels of basal and total phenoloxidase (PO), as well as lysozyme-like enzyme activities, were measured as markers of exposure. In laboratory tests, the exposure to realistic field doses of pendimethalin-based herbicides for two, seven and 21 days caused a reduction in enzyme activities in beetles from organic crops. In beetles from conventional fields, the THCs and total PO activity decreased significantly at two and seven days after the initial exposure, though no effects were recorded on basal PO and lysozyme like-enzyme activities. These differences in enzyme activities and THCs indicate that the interference of pendimethalin with immune parameters clearly depends on both the different field conditions from which the population comes and the cumulative effects of repeated applications over the time. Full article
(This article belongs to the Special Issue Biodiversity of Insect)
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Open AccessArticle
Cryoconservation of Animal Genetic Resources in Europe and Two African Countries: A Gap Analysis
Diversity 2019, 11(12), 240; https://doi.org/10.3390/d11120240 - 13 Dec 2019
Cited by 2 | Viewed by 952
Abstract
Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System [...] Read more.
Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System (DAD-IS) and information provided by gene banks from 15 European and 2 non-European countries on material stored for livestock breeds to analyze the gaps in cryomaterial collections according to species, countries and various breed categories. Out of the 2949 breeds registered in DAD-IS for these countries, 15.9% have been reported to have material stored in gene banks, but only 4.3% have material sufficient to allow breed reconstitution. The proportion of breeds with stored cryomaterial was greater than 20% for ruminants and pigs, between 10% and 20% for equids, and below 10% for rabbit and avian species. According to the results of two logistic regressions, countries show significant differences in the proportion of populations collected for cryostorage, while breeds not-at-risk are more likely to have cryomaterial preserved than are other breeds. Also, a relatively larger proportion of transboundary breeds have cryomaterial in gene banks than do local breeds, likely due in part to the fact that multiple countries have the opportunity to collect this material. These results highlight the need for increased efforts in material collection for at-risk local breeds and regional coordination on cryoconservation of material from transboundary breeds. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessArticle
Ecological Mapping in Assessing the Impact of Environmental Factors on the Aquatic Ecosystem of the Arys River Basin, South Kazakhstan
Diversity 2019, 11(12), 239; https://doi.org/10.3390/d11120239 - 12 Dec 2019
Cited by 2 | Viewed by 872
Abstract
Assessment of the water quality of the Arys River basin based on the spatial distribution of richness of phytoperiphyton communities and abiotic variables was given for the first time. Altogether, 82 species were revealed in phytoperiphyton, including Bacillariophyta of 51, Cyanobacteria of 20, [...] Read more.
Assessment of the water quality of the Arys River basin based on the spatial distribution of richness of phytoperiphyton communities and abiotic variables was given for the first time. Altogether, 82 species were revealed in phytoperiphyton, including Bacillariophyta of 51, Cyanobacteria of 20, Chlorophyta of 7, and Charophyta of 4. Cluster analysis revealed the uniqueness of the composition of periphyton communities related to the abiotic conditions. The environmental preferences of the algae indicated fresh organic pollution in the lower reaches of the Arys River and weak or moderate levels of organic pollution in the rest of the basin. The ecological mapping of chemical data generally confirmed this conclusion. According to the maps, the highest water quality was revealed in the upper stream of the basin. The middle part of the river basin had the lowest water quality in terms of transparency, nitrite-nitrogen, and nitrate-nitrogen. The downstream of the Arys was characterized by a secondary deterioration in water quality according to the Aquatic Ecosystem State Index (WESI) index. We revealed the complicated interaction between natural and anthropogenic factors that caused changes in water quality in the Arys River basin. Full article
(This article belongs to the Special Issue Freshwater Algal Diversity and Bio-Indication of Water Resources)
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Open AccessArticle
Native and Invasive Small Mammals in Urban Habitats along the Commercial Axis Connecting Benin and Niger, West Africa
Diversity 2019, 11(12), 238; https://doi.org/10.3390/d11120238 - 10 Dec 2019
Cited by 3 | Viewed by 915
Abstract
Based on compiled small mammal trapping data collected over 12 years from Benin and Niger (3701 individual records from 66 sampling sites), located in mainland Africa, we here describe the small mammal community assemblage in urban habitats along the commercial axis connecting the [...] Read more.
Based on compiled small mammal trapping data collected over 12 years from Benin and Niger (3701 individual records from 66 sampling sites), located in mainland Africa, we here describe the small mammal community assemblage in urban habitats along the commercial axis connecting the two countries, from the seaport of Cotonou to the Sahelian hinterland, with a particular focus on invasive species. In doing so, we document extant species distributions, which highlight the risks of continuing the range expansion of three synanthropic invasive rodent species, namely black rats (Rattus rattus), brown rats (R. norvegicus), and house mice (Mus musculus). Using various diversity estimates and community ecology approaches, we detect a latitudinal gradient of species richness that significantly decreased Northward. We show that shrews (Crocidura) represent a very important component of micro-mammal fauna in West African towns and villages, especially at lower latitudes. We also demonstrate that invasive and native synanthropic rodents do not distribute randomly in West Africa, which suggests that invasive species dynamics and history differ markedly, and that they involve gradual, as well as human-mediated, long distance dispersal. Patterns of segregation are also observed between native Mastomys natalensis and invasive rats R. rattus and R. norvegicus, suggesting potential native-to-invasive species turn over. Consequences of such processes, especially in terms of public health, are discussed. Full article
(This article belongs to the Special Issue Biological Invasions 2020 Horizon)
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Open AccessReview
Biotic and Abiotic Factors Associated with Colonies Mortalities of Managed Honey Bee (Apis mellifera)
Diversity 2019, 11(12), 237; https://doi.org/10.3390/d11120237 - 10 Dec 2019
Cited by 9 | Viewed by 1628
Abstract
Despite the presence of a large number of pollinators of flowering plants worldwide, the European honey bee, Apis melifera, plays the most important role in the pollination of a number of crops, including all vegetables, non-food crops and oilseed crops, decorative and [...] Read more.
Despite the presence of a large number of pollinators of flowering plants worldwide, the European honey bee, Apis melifera, plays the most important role in the pollination of a number of crops, including all vegetables, non-food crops and oilseed crops, decorative and medical plants, and others. The experience of isolated cases of complete extinction of honey bees in individual regions has shown that this phenomenon leads to a dramatic pollination crisis and reduced ability or even total inability to grow insect-pollinated crops if relying solely on native, naturally occurring pollinators. Current scientific data indicate that the global bee extinction between the Cretaceous and the Paleogene (Cretaceous-Tertiary) occurred, which led to the disappearance of flowers because they could not produce viable fruit and germinate due to lack of pollination by bees or other animals. From the Middle Ages to the present day, there has been evidence that honey bees have always overcome the adverse factors affecting them throughout the ages, after which their population has fully recovered. This fact must be treated with great care given the emergence of a new, widespread stress factor in the second half of the 20th century—intoxication of beehives with antibiotics and acaricides, and treatment of crops with pesticides. Along with acute and chronic intoxication of bees and bee products, there are other new major stressors of global importance reducing the number of bee colonies: widespread prevalence of pathogenic organisms and pest beetles, climate change and adverse climatic conditions, landscape changes and limitation of natural habitats, intensification of agricultural production, inadequate nutrition, and introduction of invasive species. This report summarizes the impact of individual negative factors on the health and behavior of bees to limit the combined effects of the above stressors. Full article
(This article belongs to the Special Issue Monitoring of Honey Bee Colony Losses)
Open AccessArticle
Crypsis Decreases with Elevation in a Lizard
Diversity 2019, 11(12), 236; https://doi.org/10.3390/d11120236 - 07 Dec 2019
Cited by 2 | Viewed by 791
Abstract
Predation usually selects for visual crypsis, the colour matching between an animal and its background. Geographic co-variation between animal and background colourations is well known, but how crypsis varies along elevational gradients remains unknown. We predict that dorsal colouration in the lizard Psammodromus [...] Read more.
Predation usually selects for visual crypsis, the colour matching between an animal and its background. Geographic co-variation between animal and background colourations is well known, but how crypsis varies along elevational gradients remains unknown. We predict that dorsal colouration in the lizard Psammodromus algirus should covary with the colour of bare soil—where this lizard is mainly found—along a 2200 m elevational gradient in Sierra Nevada (SE Spain). Moreover, we predict that crypsis should decrease with elevation for two reasons: (1) Predation pressure typically decreases with elevation, and (2) at high elevation, dorsal colouration is under conflicting selection for both crypsis and thermoregulation. By means of standardised photographies of the substratum and colourimetric measurements of lizard dorsal skin, we tested the colour matching between lizard dorsum and background. We found that, along the gradient, lizard dorsal colouration covaried with the colouration of bare soil, but not with other background elements where the lizard is rarely detected. Moreover, supporting our prediction, the degree of crypsis against bare soil decreased with elevation. Hence, our findings suggest local adaptation for crypsis in this lizard along an elevational gradient, but this local adaptation would be hindered at high elevations. Full article
(This article belongs to the Special Issue Predators as Agents of Selection and Diversification)
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Open AccessReview
Organization and Management of Conservation Programs and Research in Domestic Animal Genetic Resources
Diversity 2019, 11(12), 235; https://doi.org/10.3390/d11120235 - 06 Dec 2019
Cited by 5 | Viewed by 816
Abstract
Creating national committees for domestic animal genetic resources within genetic resource national commissions is recommended to organize in situ and ex situ conservation initiatives. In situ conservation is a high priority because it retains traditional zootechnical contexts and locations to ensure the long-term [...] Read more.
Creating national committees for domestic animal genetic resources within genetic resource national commissions is recommended to organize in situ and ex situ conservation initiatives. In situ conservation is a high priority because it retains traditional zootechnical contexts and locations to ensure the long-term survival of breeds. In situ actions can be based on subsidies, technical support, structure creation, or trademark definition. Provisional or permanent relocation of breeds may prevent immediate extinction when catastrophes, epizootics, or social conflicts compromise in situ conservation. Ex situ in vivo (animal preservation in rescue or quarantine centers) and in vitro methods (germplasm, tissues/cells, DNA/genes storage) are also potential options. Alert systems must detect emergencies and summon the national committee to implement appropriate procedures. Ex situ coordinated centers must be prepared to permanently or provisionally receive extremely endangered collections. National germplasm banks must maintain sufficient samples of national breeds (duplicated) in their collections to restore extinct populations at levels that guarantee the survival of biodiversity. A conservation management survey, describing national and international governmental and non-governmental structures, was developed. Conservation research initiatives for international domestic animal genetic resources from consortia centralize the efforts of studies on molecular, genomic or geo-evolutionary breed characterization, breed distinction, and functional gene identification. Several consortia also consider ex situ conservation relying on socioeconomic or cultural aspects. The CONBIAND network (Conservation for the Biodiversity of Local Domestic Animals for Sustainable Rural Development) exemplifies conservation efficiency maximization in a low-funding setting, integrating several Latin American consortia with international cooperation where limited human, material, and economic resources are available. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessArticle
Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment
Diversity 2019, 11(12), 234; https://doi.org/10.3390/d11120234 - 06 Dec 2019
Cited by 3 | Viewed by 1089
Abstract
Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and [...] Read more.
Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity. Full article
(This article belongs to the Special Issue Symbioses and the Biodiversity-Ecosystem Function Relationship)
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Open AccessArticle
Predicting Leaf Trait Variability as a Functional Descriptor of the Effect of Climate Change in Three Perennial Grasses
Diversity 2019, 11(12), 233; https://doi.org/10.3390/d11120233 - 06 Dec 2019
Viewed by 700
Abstract
Aims of the study: The most important trends of the current climate variability is the scarcity of rains that affects arid ecosystems. The aim of this study was to explore the variability of leaf functional traits by which grassland species survive and [...] Read more.
Aims of the study: The most important trends of the current climate variability is the scarcity of rains that affects arid ecosystems. The aim of this study was to explore the variability of leaf functional traits by which grassland species survive and resist drought and to investigate the potential link between resource use efficiency and water scarcity resistance strategies of species. Methods: Three grasses (Cenchrus ciliaris (C4), Stipa parviflora and Stipa lagascae (C3)) were established in a randomized block consisting of eleven replications. The seedlings were kept under increasing levels of water stress. In addition to their functional leaf traits, the rate of water loss and dimensional shrinkage were also measured. Key Results: Thicker and denser leaves, with higher dry matter contents, low specific leaf area and great capacity of water retention are considered among the grasses’ strategies of dehydration avoidance. Significant differences between the means of the functional traits were obtained. Furthermore, strong correlations among leaf traits were also detected (Spearman’s r exceeding 0.8). Conclusions: The results provide evidence that the studied grasses respond differently to drought by exhibiting a range of interspecific functional strategies that may ameliorate the resilience of grassland species communities under extreme drought events. Full article
(This article belongs to the Section Plant Diversity)
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Open AccessArticle
Argulus from the Pascagoula River, MS, USA, with an Emphasis on Those of the Threatened Gulf Sturgeon, Acipenser oxyrinchus desotoi
Diversity 2019, 11(12), 232; https://doi.org/10.3390/d11120232 - 05 Dec 2019
Viewed by 663
Abstract
Species of Argulus (Branchiura Thorell, 1864) are common ectoparasites of freshwater, estuarine, and marine fishes. Argulid identification and taxonomy is often confusing because many species are reported to parasitize multiple host species, have similar morphological characters, and come from various salinity regimes. Gulf [...] Read more.
Species of Argulus (Branchiura Thorell, 1864) are common ectoparasites of freshwater, estuarine, and marine fishes. Argulid identification and taxonomy is often confusing because many species are reported to parasitize multiple host species, have similar morphological characters, and come from various salinity regimes. Gulf sturgeon is an anadromous fish natal to drainages in the north-central Gulf of Mexico, and as with many endangered species, has a poorly documented parasite community. During Gulf sturgeon tagging and monitoring studies (2016–2019) in the Pascagoula River, MS, USA, species of Argulus were collected from Gulf sturgeon as well as other incidentally captured fishes. Argulus flavescens Wilson, 1916 was found on Gulf sturgeon and flathead catfish, Argulus americanus Wilson, 1902 on bowfin, and Argulus bicolor Bere, 1936 on Atlantic stingray. We provide morphological details and measurements for these species as well as the first confirmed 28S rDNA molecular data. Argulus flavescens was more abundant and prevalent on larger Gulf sturgeon and on sturgeon captured in freshwater rather than estuarine habitats. Our results indicate that A. flacescens may not tolerate estuarine salinities and that the anadromous life-history pattern of Gulf sturgeon could help rid them of A. flavescens when they emigrate from their riverine habitats. Full article
(This article belongs to the Special Issue Taxonomy and Diversity of Aquaculture and Fisheries Parasites)
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Open AccessArticle
Nitrogen Fixing and Phosphate Mineralizing Bacterial Communities in Sweet Potato Rhizosphere Show a Genotype-Dependent Distribution
Diversity 2019, 11(12), 231; https://doi.org/10.3390/d11120231 - 03 Dec 2019
Cited by 2 | Viewed by 693
Abstract
We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total [...] Read more.
We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total community DNA was extracted from the rhizosphere and analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), based on the alkaline phosphatase coding gene (alp gene) and on the nitrogenase coding gene (nifH gene). The cluster analysis based on DGGE showed that plant age slightly influenced the bacterial community related to phosphate mineralization in the rhizosphere of IPB-137, although it did not affect the bacterial community related to nitrogen fixation. The statistical analysis of DGGE fingerprints (Permutation test, p ≤ 0.05) showed that nitrogen-fixing bacterial community of IPB-052 statistically differed from genotypes IPB-149 and IPB-137 after six months of planting. The bacterial community of IPB-137 rhizosphere analyzed by alp gene also showed significant differences when compared to IPB-149 in both sampling times (p ≤ 0.05). In addition, alp gene copy numbers significantly increased in abundance in the rhizosphere of IPB-137 after six months of planting. Therefore, plant genotype should be considered in the biofertilization of sweet potato. Full article
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Open AccessArticle
Geographical Range Extension of the Spotfin burrfish, Chilomycterus reticulatus (L. 1758), in the Canary Islands: A Response to Ocean Warming?
Diversity 2019, 11(12), 230; https://doi.org/10.3390/d11120230 - 29 Nov 2019
Cited by 2 | Viewed by 795
Abstract
In recent decades, numerous marine species have changed their distribution ranges due to ocean warming. The Spotfin burrfish, Chilomycterus reticulatus, is a reef fish with a global distribution along tropical, subtropical and warm-temperate areas of the Pacific, Indian and Atlantic oceans. In [...] Read more.
In recent decades, numerous marine species have changed their distribution ranges due to ocean warming. The Spotfin burrfish, Chilomycterus reticulatus, is a reef fish with a global distribution along tropical, subtropical and warm-temperate areas of the Pacific, Indian and Atlantic oceans. In this work, we analyzed the presence of this species, between 1990 and 2019, at two islands of the Canarian Archipelago under varying oceanographic conditions: El Hierro (the westernmost island, under more tropical conditions) and Gran Canaria (a central-east island, under more cooler conditions). We expected that, under increased ocean temperatures in recent decades, the number of sightings has increased in Gran Canaria relative to El Hierro. We compiled information from different sources, including interviews and local citizenship databases. A total of 534 sightings were reported: 38.58% from El Hierro and 61.43% from Gran Canaria. The number of sightings on Gran Canaria has significantly increased through time, at a rate of 0.1 sightings per year; at El Hierro, however, the number of sightings has not significantly changed over time. Sea Surface Temperature has linearly increased in both El Hierro and Gran Canaria islands over the last three decades. Positive Sea Surface Temperature anomalies, particularly in 1998 and 2010, including high winter minimum temperatures, provide an ideal oceanographic context to favour the arrival of new individuals and, consequently, the increase in the number of sightings in Gran Canaria. Still, potential donor areas of fish recruits remain unknown. Full article
(This article belongs to the Special Issue Global Change Effects on Marine Benthos)
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Open AccessArticle
Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds
Diversity 2019, 11(12), 229; https://doi.org/10.3390/d11120229 - 28 Nov 2019
Cited by 3 | Viewed by 1271
Abstract
In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. [...] Read more.
In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. Based on these similarities, most breeds were clearly differentiated, except for two breeds (Deep Red and Improved Red and White) that have recently been derived from the MRY breed, and for the Dutch Friesian and Dutch Friesian Red, which have frequently exchanged bulls. Optimal contribution selection (OCS) was used to construct core sets of bulls with a minimized similarity. The composition of the gene bank appeared to be partly optimized in the semen collection process, i.e., the mean similarity within breeds based on the current number of straws per bull was 0.32% to 1.49% lower than when each bull would have contributed equally. Mean similarity could be further reduced within core sets by 0.34% to 2.79% using OCS. Material not needed for the core sets can be made available for supporting in situ populations and for research. Our findings provide insight in genetic diversity in Dutch cattle breeds and help to prioritize material in gene banking. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessArticle
Microplastic Contamination Has Limited Effects on Coral Fertilisation and Larvae
Diversity 2019, 11(12), 228; https://doi.org/10.3390/d11120228 - 28 Nov 2019
Cited by 4 | Viewed by 1635
Abstract
Microplastics are ubiquitous throughout the world’s oceans and contaminate coral reef ecosystems. There is evidence of microplastic ingestion by corals and passive contact with coral tissues, causing adverse health effects that include energy expenditure for particle removal from the tissue surface, as well [...] Read more.
Microplastics are ubiquitous throughout the world’s oceans and contaminate coral reef ecosystems. There is evidence of microplastic ingestion by corals and passive contact with coral tissues, causing adverse health effects that include energy expenditure for particle removal from the tissue surface, as well as reduced growth, tissue bleaching, and necrosis. Here, it was examined whether microplastic contamination impairs the success of gamete fertilisation, embryo development and larval settlement of the reef-building coral Acropora tenuis. Coral gametes and larvae were exposed to fifteen microplastic treatments using two types of plastic: (1) weathered polypropylene particles and (2) spherical polyethylene microbeads. The treatments ranged from five to 50 polypropylene pieces L−1 and 25 to 200 microbeads L−1. Fertilisation was only negatively affected by the largest weathered microplastics (2 mm2), but the effects were not dose dependent. Embryo development and larval settlement were not significantly impacted by either microplastic type. The study shows that moderate–high levels of marine microplastic contamination, specifically particles <2 mm2, will not substantially interfere with the success of critical early life coral processes. Full article
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Open AccessCommunication
First Record of Amphioxus Branchiostoma californiense (Amphioxiformes: Branchiostomatidae) Adjacent to a Shallow Submarine Hydrothermal System at Banderas Bay (Mexico)
Diversity 2019, 11(12), 227; https://doi.org/10.3390/d11120227 - 28 Nov 2019
Cited by 1 | Viewed by 795
Abstract
Shallow submarine hydrothermal vent systems assume differentiated environmental conditions. Some specimens of Branchiostoma californiense were found in the sediments of the influence area of the shallow hydrothermal venting in Punta Mita. This is the only lancelet species registered for the Mexican Pacific. The [...] Read more.
Shallow submarine hydrothermal vent systems assume differentiated environmental conditions. Some specimens of Branchiostoma californiense were found in the sediments of the influence area of the shallow hydrothermal venting in Punta Mita. This is the only lancelet species registered for the Mexican Pacific. The meristic and morphometric characteristics of the organisms first collected in unconsolidated sediments of this shallow system were reviewed, in order to determine the species. We confirm that it is the same species. This represents the first record of it for both the Banderas bay and in the influence area of a shallow hydrothermal system. Full article
(This article belongs to the Section Marine Diversity)
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Open AccessArticle
A Long-Term Demographic Analysis of Spotted Turtles (Clemmys guttata) in Illinois Using Matrix Models
Diversity 2019, 11(12), 226; https://doi.org/10.3390/d11120226 - 26 Nov 2019
Cited by 1 | Viewed by 1243
Abstract
Matrix models and perturbation analyses provide a useful framework for evaluating demographic vital rates crucial to maintaining population growth. Determining which vital rates most influence population growth is necessary for effective management of long-lived organisms facing population declines. In Illinois, the state-endangered Spotted [...] Read more.
Matrix models and perturbation analyses provide a useful framework for evaluating demographic vital rates crucial to maintaining population growth. Determining which vital rates most influence population growth is necessary for effective management of long-lived organisms facing population declines. In Illinois, the state-endangered Spotted Turtle (Clemmys guttata) occurs in two distinct populations, and management can benefit from an understanding of its demographic behavior. We conducted a mark–recapture study on both populations in 2015 and 2016 and used historical mark–recapture data from 1988 to 2010 to determine female age-specific survival and fecundity rates. Survival increased significantly with age, and age-specific reproductive output and fecundity were >1.0. However, both populations exhibited net reproductive rates below replacement levels, and one population had a negative growth rate. Summed elasticities for all adult age classes indicate adult survival has the highest proportional impact on population growth. We found evidence of demographic divergence between the two populations, and thus the prioritization of vital rates varied somewhat between sites, with a relatively higher emphasis on juvenile and young adult survival for one population. We recommend conservation actions such as habitat management and predator control, which will have positive impacts across stage classes. Full article
(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)
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Open AccessArticle
Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of Mycobacterium ulcerans and Multiple Wolbachia Sequence Types Revealed by Metagenomics
Diversity 2019, 11(12), 225; https://doi.org/10.3390/d11120225 - 25 Nov 2019
Cited by 1 | Viewed by 977
Abstract
Buruli ulcer (BU), caused by Mycobacterium ulcerans, is a neglected tropical disease associated with freshwater habitats. A variety of limnic organisms harbor this pathogen, including aquatic bugs (Hemiptera: Heteroptera), which have been hypothesized to be epidemiologically important reservoirs. Aquatic Hemiptera exhibit high [...] Read more.
Buruli ulcer (BU), caused by Mycobacterium ulcerans, is a neglected tropical disease associated with freshwater habitats. A variety of limnic organisms harbor this pathogen, including aquatic bugs (Hemiptera: Heteroptera), which have been hypothesized to be epidemiologically important reservoirs. Aquatic Hemiptera exhibit high levels of diversity in the tropics, but species identification remains challenging. In this study, we collected aquatic bugs from emerging foci of BU in the Southwest Region of Cameroon, which were identified using morphological and molecular methods. The bugs were screened for mycobacterial DNA and a selection of 20 mycobacteria-positive specimens from the families Gerridae and Veliidae were subjected to next-generation sequencing. Only one individual revealed putative M. ulcerans DNA, but all specimens contained sequences from the widespread alpha-proteobacterial symbiont, Wolbachia. Phylogenetic analysis placed the Wolbachia sequences into supergroups A, B, and F. Circularized mitogenomes were obtained for seven gerrids and two veliids, the first from these families for the African continent. This study suggests that aquatic Hemiptera may have a minor role (if any) in the spread of BU in Southwest Cameroon. Our metagenomic analysis provides new insights into the incursion of Wolbachia into aquatic environments and generated valuable resources to aid molecular taxonomic studies of aquatic Hemiptera. Full article
(This article belongs to the Special Issue Insect Symbiosis)
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Open AccessArticle
Diversity of Species and Susceptibility Phenotypes toward Commercially Available Fungicides of Cultivable Fungi Colonizing Bones of Ursus spelaeus on Display in Niedźwiedzia Cave (Kletno, Poland)
Diversity 2019, 11(12), 224; https://doi.org/10.3390/d11120224 - 23 Nov 2019
Cited by 4 | Viewed by 841
Abstract
Underground ecosystems are one of the most inhospitable places for microorganism development and function. Therefore, any organic matter located in these areas can stimulate fungal growth. The main purpose of this study was to find the best solution to effectively preserve (without relapses) [...] Read more.
Underground ecosystems are one of the most inhospitable places for microorganism development and function. Therefore, any organic matter located in these areas can stimulate fungal growth. The main purpose of this study was to find the best solution to effectively preserve (without relapses) paleolithic bones of cave bear (Ursus spelaeus) exhibited in cave without any negative influence on the cave environment. To achieve this aim, unambiguous identification of fungal species and its susceptibility tests toward fungicidal preparations were performed. Fungi were identified based on phenotypic tests and the internal transcribed spacer (ITS) region analysis. The antifungal activity of three preparations (Pufmax, Boramon and Devor Mousse) was evaluated by microdilution assay (protocol M38-A2) and spot tests assay. Phenotypic and molecular research showed that bones were colonized by 11 fungal species: Absidia glauca, Aspergillus fumigatus, Chrysosporium merdarium, Fusarium cerealis, Mortierella alpina, Mucor aligarensis, M. plumbeus, Penicillium chrysogenum, P. expansum, Sarocladium strictum and Scopulariopsis candida. All of the tested preparations were the most active against C. merdarium. In turn, M. plumbeus, M. aligarensis, M. alpina and A. glauca were the least susceptible. The highest antifungal activity was shown for Pufmax (minimum inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) values were in the range of 0.16–0.63% and 1.25–2.50%, respectively). The lowest fungicidal effect was observed for Boramon (MICs and MFCs in the range of 2.5–10% and 5–20%, respectively). Devor Mousse and Pufmax preparations showed fungicidal activity at the concentrations in the range of 1.25–5%. Susceptibility profiles were also confirmed based on spot tests assay. Our study allows for unambiguously identifying isolated fungi and assessing their susceptibility to commercially available fungicides, to prevent fungal outbreak. Full article
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Open AccessArticle
Germinable Soil Seed Bank in Biancana Badlands
Diversity 2019, 11(12), 223; https://doi.org/10.3390/d11120223 - 23 Nov 2019
Viewed by 699
Abstract
Seed banks are important for understanding vegetation dynamics and habitat regeneration potential. Biancana badlands are vanishing landscapes where recurring and non-recurring management has been advocated to restore vegetation. Here, we investigated germinable seed bank structure and composition of a biancana badland in central [...] Read more.
Seed banks are important for understanding vegetation dynamics and habitat regeneration potential. Biancana badlands are vanishing landscapes where recurring and non-recurring management has been advocated to restore vegetation. Here, we investigated germinable seed bank structure and composition of a biancana badland in central Italy and evaluated the relationship between the standing vegetation and soil seed bank. We identified four land cover classes in five biancana badlands of Tuscany (central Italy) and collected data from 132 vegetation plots and 660 soil cores. We recorded 117 species in the standing vegetation. The seedlings that emerged from the soil samples, mostly annual species, numbered 183 and belonged to 31 taxa (392.5 seedlings/m−2 on average across the four land cover classes). Standing vegetation showed an aggregated spatial pattern with distinct communities while the seed bank showed a less aggregated spatial pattern. The similarity between the seed bank and standing vegetation was low. In contrast with the features generally found for disturbed and pioneer communities, but in line with seed bank characteristics of other badlands, the seed bank was particularly poor in species. Full article
(This article belongs to the Section Plant Diversity)
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Open AccessArticle
No Change Detected in Culturable Fungal Assemblages on Cave Walls in Eastern Canada with the Introduction of Pseudogymnoascus destructans
Diversity 2019, 11(12), 222; https://doi.org/10.3390/d11120222 - 23 Nov 2019
Cited by 2 | Viewed by 810
Abstract
Studies of fungi in caves have become increasingly important with the advent of white-nose syndrome (WNS), a disease caused by the invasive fungus Pseudogymnoascus destructans (Pd) that has killed an estimated 6.5 million North American bats. We swabbed cave walls in [...] Read more.
Studies of fungi in caves have become increasingly important with the advent of white-nose syndrome (WNS), a disease caused by the invasive fungus Pseudogymnoascus destructans (Pd) that has killed an estimated 6.5 million North American bats. We swabbed cave walls in New Brunswick, Canada, in 2012 and 2015 to determine whether the culturable fungal assemblage on cave walls changed after the introduction of Pd and subsequent decrease in hibernating bat populations. We also compared fungal assemblages on cave walls to previous studies on the fungal assemblages of arthropods and hibernating bats in the same sites. The fungal diversity of bats and cave walls was more similar than on arthropods. The diversity and composition of fungal assemblages on cave walls was significantly different among media types and sites but did not differ over time. Therefore, no change in the culturable fungal assemblage present on cave walls was detected with the introduction of Pd and subsequent disappearance of the hibernating bat population over a 3-year period. This suggests that fungi documented in caves in the region prior to the outbreak of Pd do not require regular transmission of spores by bats to maintain fungal diversity at these sites. Full article
(This article belongs to the Section Microbial Diversity and Culture Collections)
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Open AccessCommunication
Morphometric Evaluation of Phenotypic Groups of Creole Cattle of Southern Ecuador
Diversity 2019, 11(12), 221; https://doi.org/10.3390/d11120221 - 20 Nov 2019
Cited by 1 | Viewed by 908
Abstract
The breeding of creole cattle from the southern region of Ecuador, also known as Criollo Lojano, is a source of economic support and work for the communities located in the remote areas of the Andes mountains in this region. These cattle are grouped [...] Read more.
The breeding of creole cattle from the southern region of Ecuador, also known as Criollo Lojano, is a source of economic support and work for the communities located in the remote areas of the Andes mountains in this region. These cattle are grouped into four biotypes based on their phenotypic characteristics: Negro Lojano, Encerado, Colorado, and Cajamarca or Pintado. This study analyzes the morphometric variability of these creole cattle using least squares means (LSM) and restricted maximum likelihood Restricted Maximum Likelihood (REML) variance components. The evaluation parameters used to characterize these cattle were live weight plus 15 morphometric characteristics and nine morphometric indexes. The measurements came from 151 adult animals (28 male and 123 females). With the exception of Height at Withers (P = 0.06), the other morphometric characteristics do not show significant difference among these creole biotypes. Sexual dimorphism was found in live weight, thoracic circumference, height at withers, chest width, length of thorax, length of body, depth of thorax, depth of abdomen, length of head, and length of horns (P < 0.05). The adult Creole Lojano has an average live weight of 288 ± 12.9 kg (mean ± standard error), The Cephalic index is 45.6, the Corporal index is 115.9, the Pelvic index is 90.5, the Thoracic index is 58.3, the Proportionality index is 62.6, the Thoracic Capacity index is 2.1, the Lower Leg–Thoracic index is 9.9, the Transverse Pelvic index is 34.7, and the Pelvic Length index is 38.4. This creole bovine breed presents 4 biotypes that are similar; there are differences in the analysis with respect to sex (males are higher in 10 of the 16 characteristics analyzed); and on the basis of the indexes, this animal is small, has a triangular head, is longilinear with a long and narrow hip. It is a dual-purpose milk type with the exception of the Colorado biotype which is a dual purpose meat type. Full article
(This article belongs to the Special Issue Conservation of Rare Breeds of Livestock)
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Open AccessArticle
Chloroplast Genome-Based Hypervariable Markers for Rapid Authentication of Six Korean Pyropia Species
Diversity 2019, 11(12), 220; https://doi.org/10.3390/d11120220 - 20 Nov 2019
Cited by 1 | Viewed by 684
Abstract
We previously established that polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis using partial plastid rbcL and mitochondrial trnC–trnP gene sequences can be used to distinguish the six representative Pyropia species produced via mariculture in Korea. In this study, we develop progressive InDel [...] Read more.
We previously established that polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis using partial plastid rbcL and mitochondrial trnC–trnP gene sequences can be used to distinguish the six representative Pyropia species produced via mariculture in Korea. In this study, we develop progressive InDel markers by comparing seven complete Pyropia chloroplast genomes obtained from The National Center of Biotechnology Informnation (NCBI) GenBank. Comparative analyses of nucleotide diversity among the genomes revealed seven hypervariable sites (cemA, rps13, trnM-argB, petD-petB, trnR-trnQ, ccs1-orf24, and ycf12-ftrB) among 637 sliding windows with nucleotide diversity > 0.025 (Pi). These sites included two genes and five gene-intergenic regions, three of which (cemA, trnM-argB, trnR-trnQ) showed complete amplification for all six test species. Finally, trnM-argB, an InDel-variable locus with high discriminatory power, was selected as a DNA barcode candidate. These results suggest that the obtained trnM-argB region can be used for the effective exploration of the variation present in six Korean Pyropia and for further evolutionary, phylogenetic, barcoding and genetic engineering studies of Pyropia species. Full article
(This article belongs to the Section Marine Diversity)
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