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Diversity, Volume 10, Issue 4 (December 2018)

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Cover Story (view full-size image) The Australian Cherax destructor is one of the last alien crayfish introduced in Italy. In the [...] Read more.
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Open AccessArticle Effectiveness of DNA Barcoding in Speyeria Butterflies at Small Geographic Scales
Diversity 2018, 10(4), 130; https://doi.org/10.3390/d10040130
Received: 15 October 2018 / Revised: 29 November 2018 / Accepted: 10 December 2018 / Published: 14 December 2018
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Abstract
North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of [...] Read more.
North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of sympatric species. Recent molecular work has found not all Speyeria species to be monophyletic, which could be explained by improper species definitions, incomplete lineage sorting, or ongoing hybridization and introgression. However, these studies involved broad geographic sampling where molecular markers such as the DNA barcode may be especially subject to incomplete lineage sorting. Here we focus on a more local scale, analyzing the mitochondrial gene cytochrome oxidase subunit I (CoI) to test whether this marker recovers four sympatric Speyeria species: adiaste (W. H. Edwards, 1864), callippe (Boisduval, 1852), coronis (Behr, 1864), and zerene (Boisduval, 1852), in the greater San Francisco Bay Area. We found that CoI works well to separate all four species. Subspecies were less well-defined, with the S. adiaste subspecies clustering separately, but more mixed for the S. zerene and S. callippe subspecies. Overall, our analyses illustrate the utility of the DNA barcode for separating the Speyeria species and suggest further studies to investigate different geographic scales in order to elucidate genetic diversity patterns in this genus in North America. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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Open AccessArticle Community Ecology and Phylogeography of Bats in the Guianan Savannas of Northern South America
Diversity 2018, 10(4), 129; https://doi.org/10.3390/d10040129
Received: 20 September 2018 / Revised: 21 November 2018 / Accepted: 4 December 2018 / Published: 13 December 2018
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Abstract
The Guiana Shield of South America contains savannas within one of the largest contiguous expanses of pristine tropical rainforest remaining in the world, but biodiversity in the grasslands is poorly known. In lowland Neotropical areas, bats typically comprise the most species-rich group of [...] Read more.
The Guiana Shield of South America contains savannas within one of the largest contiguous expanses of pristine tropical rainforest remaining in the world, but biodiversity in the grasslands is poorly known. In lowland Neotropical areas, bats typically comprise the most species-rich group of mammals. We compare the bat faunal community and phylogeography in the savanna habitats of the Llanos in Venezuela, Rupununi in Guyana, and Sipaliwini in Suriname. Measures of species diversity and relative abundance from standardized field survey methodology enable comparison among these three grassland regions. Genetic variation is summarized by DNA barcoding to examine biogeographic patterns across larger forest–savanna landscapes. A total of 76 species of bats is documented, of which 18 species are reported from all 3 savannas and 30 species are reported from only 1 of the savannas. Endemism is low with 5 taxa restricted primarily to dry, open habitats. However, 7 other species have divergent phylogeographic lineages associated with savanna populations. Although bat species are usually distributed over wide regions of the Neotropics, the habitat mosaics of the Guiana Shield have different faunal assemblages. Going back into the Miocene, the contractions and expansions of forest–savanna paleoenvironments over time have contributed to speciation and the current high levels of biodiversity in South America. Full article
(This article belongs to the Special Issue Diversity and Conservation of Bats)
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Open AccessArticle Development of PVC Dispensers for Long-Lasting Release of Attractants for the Control of Invasive Crayfish Populations
Diversity 2018, 10(4), 128; https://doi.org/10.3390/d10040128
Received: 29 October 2018 / Revised: 4 December 2018 / Accepted: 5 December 2018 / Published: 7 December 2018
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Abstract
Invasive alien species (IAS) are considered one of the major threats to biodiversity worldwide, thus requiring severe control strategies. Based on the promising results obtained in the field of insect pest management with polyvinyl chloride (PVC) for long-lasting release of attractants, the main [...] Read more.
Invasive alien species (IAS) are considered one of the major threats to biodiversity worldwide, thus requiring severe control strategies. Based on the promising results obtained in the field of insect pest management with polyvinyl chloride (PVC) for long-lasting release of attractants, the main aim of this study was to ascertain the efficacy of PVC/attractant dispensers also in the aquatic environment. Therefore, we developed PVC/food dispensers and evaluated their attractiveness, by means of behavioural bioassays on whole animals, over a 60-day period of continuous use towards the red swamp crayfish Procambarus clarkii, one of the top 100 worst IAS. The attractiveness in PVC of trehalose, leucine and taurocholic acid was also tested. Our results show that the PVC dispensers release the food and are strongly attractive for crayfish over a prolonged time, even if their effectiveness depends on the storage conditions: From 18 days when stored underwater at 23 °C up to 50 days when stored out of the water at −20 °C. Besides, trehalose, leucine and taurocholic acid in PVC resulted in reliable attractants for P. clarkii. The development of PVC dispensers for long-lasting release of attractants may help improve the efficiency of mass trapping strategies in the management and control of invasive crayfish. Full article
(This article belongs to the Special Issue Management and Control of Invasive Crayfish (Crustacea))
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Open AccessArticle Marine Heterobranchia (Gastropoda, Mollusca) in Bunaken National Park, North Sulawesi, Indonesia—A Follow-Up Diversity Study
Diversity 2018, 10(4), 127; https://doi.org/10.3390/d10040127
Received: 28 July 2018 / Revised: 23 November 2018 / Accepted: 23 November 2018 / Published: 4 December 2018
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Abstract
Bunaken National Park has been surveyed for a fourth time in 14 years, in an attempt to establish the species composition of heterobranch sea slugs in a baseline study for monitoring programs and protection of this special park. These molluscs are potentially good [...] Read more.
Bunaken National Park has been surveyed for a fourth time in 14 years, in an attempt to establish the species composition of heterobranch sea slugs in a baseline study for monitoring programs and protection of this special park. These molluscs are potentially good indicators of the health of an ecosystem, as many are species-specific predators on a huge variety of marine benthic and sessile invertebrates from almost every taxonomic group. Additionally, they are known to contain bio-compounds of significance in the pharmaceutical industry. It is therefore of paramount importance not only to document the species composition from a zoogeographic point of view, but to assist in their protection for the future, both in terms of economics and aesthetics. These four surveys have documented more than 200 species, with an approximate 50% of each collection found only on that survey and not re-collected. Many species new to science have also been documented, highlighting the lack of knowledge in this field. Full article
(This article belongs to the Section Marine Diversity)
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Open AccessCommunication The Red Alien vs. the Blue Destructor: The Eradication of Cherax destructor by Procambarus clarkii in Latium (Central Italy)
Diversity 2018, 10(4), 126; https://doi.org/10.3390/d10040126
Received: 31 October 2018 / Revised: 24 November 2018 / Accepted: 29 November 2018 / Published: 30 November 2018
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Abstract
Cherax destructor is a crayfish endemic to south-eastern Australia and one of the last alien crayfish to be introduced in Italy. In the Laghi di Ninfa Natural Reserve (Latium region, Central Italy), the species was probably introduced in 1999, but only reported for [...] Read more.
Cherax destructor is a crayfish endemic to south-eastern Australia and one of the last alien crayfish to be introduced in Italy. In the Laghi di Ninfa Natural Reserve (Latium region, Central Italy), the species was probably introduced in 1999, but only reported for the first time in 2008. Nearby this area, the most widespread alien crayfish is the red swamp crayfish Procambarus clarkii. In the Natural Reserve, between 2008 and 2013 and during spring and summer, crayfish sampling was carried out with baited traps to assess the distribution of C. destructor and its possible relationship with P. clarkii. Cherax destructor was first recorded in 2008; few P. clarkii were detected in the cultivation ponds where C. destructor was present in 2012 and 2013. Moreover, crayfish plague analyses evidenced a positive result in two out of the 12 sampled P. clarkii. Cherax destructor is now completely absent from the Natural Reserve, while P. clarkii has spread in the area and was probably responsible for this eradication since C. destructor is vulnerable to crayfish plague which was also detected in the area. An ecosystem restoration project in the area favoured the spread of. P. clarkii; the implications of this intervention are discussed. Full article
(This article belongs to the Special Issue Management and Control of Invasive Crayfish (Crustacea))
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Open AccessArticle Adaptations by Zostera marina Dominated Seagrass Meadows in Response to Water Quality and Climate Forcing
Diversity 2018, 10(4), 125; https://doi.org/10.3390/d10040125
Received: 27 September 2018 / Revised: 16 November 2018 / Accepted: 21 November 2018 / Published: 27 November 2018
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Abstract
Global assessments of seagrass declines have documented accelerating rates of loss due to anthropogenic sediment and nutrient loadings, resulting in poor water quality. More recently, global temperature increases have emerged as additional major stressors. Seagrass changes in the Chesapeake Bay, USA provide important [...] Read more.
Global assessments of seagrass declines have documented accelerating rates of loss due to anthropogenic sediment and nutrient loadings, resulting in poor water quality. More recently, global temperature increases have emerged as additional major stressors. Seagrass changes in the Chesapeake Bay, USA provide important examples of not only the effects of human disturbance and climate forcing on seagrass loss, but also meadow recovery and resiliency. In the York River sub-tributary of the Chesapeake Bay, the meadows have been monitored intensively using annual aerial imagery, monthly transect surveys, and continuous water quality measurements. Here, Zostera marina has been demonstrating a shift in its historical growth patterns, with its biomass peaking earlier in the growing season and summer declines beginning earlier. We found an increasing trend in the length of the most stressful high temperature summer period, increasing by 22 days since 1950. Over the past 20 years, Z. marina’s abundance has exhibited periods of decline followed by recovery, with recovery years associated with greater spring water clarity and less time spent at water temperatures > 28 °C. Although human disturbance and climatic factors have been altering these seagrass meadows, resilience has been evident by an increase in reproductive output and regrowth from Z. marina seedlings following declines, as well as expansions of Ruppia maritima into areas previously dominated by Z. marina. Full article
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Open AccessArticle The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers
Diversity 2018, 10(4), 124; https://doi.org/10.3390/d10040124
Received: 1 November 2018 / Revised: 16 November 2018 / Accepted: 20 November 2018 / Published: 27 November 2018
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Abstract
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that [...] Read more.
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis. Full article
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Open AccessArticle Comparing Medicinal Uses of Cochlospermaceae throughout Its Geographic Range with Insights from Molecular Phylogenetics
Diversity 2018, 10(4), 123; https://doi.org/10.3390/d10040123
Received: 13 September 2018 / Revised: 2 November 2018 / Accepted: 8 November 2018 / Published: 15 November 2018
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Abstract
Species of the Cochlospermaceae, a small mostly pantropical plant family, were evaluated at a continental scale for medicinal uses in traditional medicine. This ethnobotanical information was placed in a phylogenetic framework to make informed predictions in the search for new medicines and bioactive [...] Read more.
Species of the Cochlospermaceae, a small mostly pantropical plant family, were evaluated at a continental scale for medicinal uses in traditional medicine. This ethnobotanical information was placed in a phylogenetic framework to make informed predictions in the search for new medicines and bioactive compounds. Medicinal plant-use data were mapped onto a molecular phylogeny based on DNA sequences of nuclear and chloroplast markers. Associations of medicinal uses among closely related species occurring in different geographic regions and among diverse cultures were evaluated. The most common medicinal uses for these species are those used to treat skin ailments, gastro-intestinal problems, malaria, and liver issues. The plant species with the most numerous uses is Cochlospermum tinctorium, which occurs primarily in West Africa. Closely related species being used by cultural groups in different geographic regions to treat the same illnesses suggests the presence of bioactive compounds with potential biomedical value, since they may represent independent discoveries of similar medicinally-active compounds. This leads to the speculation that those closely related species not currently being used to treat these ailments may also contain identical or similar medicinally-active compounds and are worthy of laboratory investigations. Full article
(This article belongs to the Special Issue Phylogenetic Exploration of Medicinal Plants Diversity)
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Open AccessArticle Limited Cross-Shelf Variation in the Growth of Three Branching Corals on Australia’s Great Barrier Reef
Diversity 2018, 10(4), 122; https://doi.org/10.3390/d10040122
Received: 16 September 2018 / Revised: 31 October 2018 / Accepted: 7 November 2018 / Published: 12 November 2018
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Abstract
Pronounced differences exist in the biodiversity and structure of coral reef assemblages with increasing distance from shore, which may be expected given marked cross-shelf gradients in environmental conditions. Cross-shelf variation in the abundance of coral reef organisms is likely to be caused, at [...] Read more.
Pronounced differences exist in the biodiversity and structure of coral reef assemblages with increasing distance from shore, which may be expected given marked cross-shelf gradients in environmental conditions. Cross-shelf variation in the abundance of coral reef organisms is likely to be caused, at least in part, by differences in demography (e.g., growth and survival), though this has rarely been tested. This study quantified growth of three distinct branching coral taxa (Acropora nasuta, Pocillopora spp. and Stylophora pistillata) at six locations on Australia’s Great Barrier Reef (GBR), encompassing inshore, mid-shelf and outer-shelf reefs. Replicate colonies (0–15 colonies per species, per reef) were stained using Alizarin Red in December 2015 and retrieved one year later to quantify linear extension on replicate branches for each colony. Annual linear extension varied within and among coral taxa, with pronounced differences among reefs. For A. nasuta. and S. pistillata, growth rates were highest at one of the inshore reefs, Orpheus Island. However, inter-reef differences in linear extension were not explained by shelf position. Based on differences in skeletal density, which did vary according to shelf position, branching corals at the inshore sites may actually have higher rates of calcification compared to conspecifics on mid-and outer-shelf reefs. This study shows that growth of branching corals is not lower at inshore sites (and perhaps even higher) compared to sites at mid-shelf and outer reefs, despite generally higher levels of sedimentation and turbidity. Full article
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Open AccessArticle Growth and Survival of Endemic Cacti under Different Substrate Types and Sun Exposures for Their Optimal Establishment in Northeastern Mexico
Diversity 2018, 10(4), 121; https://doi.org/10.3390/d10040121
Received: 21 October 2018 / Revised: 7 November 2018 / Accepted: 7 November 2018 / Published: 10 November 2018
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Abstract
Cactaceae are subject to strong anthropogenic pressure, which motivates the search of strategies for its conservation. This paper aimed to evaluate the survival and growth of eight native species from northeastern Mexico, in order to propose their in-situ conservation, applying three substrates (perlite/peat-moss, [...] Read more.
Cactaceae are subject to strong anthropogenic pressure, which motivates the search of strategies for its conservation. This paper aimed to evaluate the survival and growth of eight native species from northeastern Mexico, in order to propose their in-situ conservation, applying three substrates (perlite/peat-moss, zeolite/peat-moss and natural soil), in two sun exposures (west and east). The variability of both survival and growth resulted dependent on substrate type and sun exposure. Astrophytum myriostigma presented higher diameter at eastern aspects (51.20 and 42.63 mm on zeolite/peat-moss and perlite/peat-moss, respectively), and the higher heights were also registered at eastern aspects, with Sclerocactus scheeri (7.38.cm on perlite/peat-moss and 6.98 cm on natural soil) and A. myriostigma (6.8 cm on zeolite/peat-moss and 6.08 cm on perlite/peat-moss). As for survival, the highest value (100%) was recorded with the treatments of West-Zeolite/peat-moss and East-Perlite/peat-moss, in six of the eight species evaluated (A. myriostigma, Acharagma roseana, Escobaria dasyacantha, S. scheeri and Mammillaria prolifera), while the lowest value (0%) was recorded with M. plumosa in the three western combinations. The best growth and survival responses were observed in A. myriostigma and S. scheeri under east exposure and zeolite, being the best combination, to be considered for their optimal establishment. Full article
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Open AccessArticle Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging
Diversity 2018, 10(4), 120; https://doi.org/10.3390/d10040120
Received: 9 September 2018 / Revised: 29 October 2018 / Accepted: 30 October 2018 / Published: 2 November 2018
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Abstract
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across [...] Read more.
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels. Full article
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Open AccessReview Urban Re-Greening: A Case Study in Multi-Trophic Biodiversity and Ecosystem Functioning in a Post-Industrial Landscape
Diversity 2018, 10(4), 119; https://doi.org/10.3390/d10040119
Received: 31 July 2018 / Revised: 5 October 2018 / Accepted: 9 October 2018 / Published: 1 November 2018
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Abstract
The biodiversity of urban and post-industrial ecosystems is a highly relevant and growing new frontier in ecological research. Even so, the functionality of these ecosystems may not always be successfully predicted based on prior biodiversity and ecosystem functioning theory. Indeed, evidence suggests that [...] Read more.
The biodiversity of urban and post-industrial ecosystems is a highly relevant and growing new frontier in ecological research. Even so, the functionality of these ecosystems may not always be successfully predicted based on prior biodiversity and ecosystem functioning theory. Indeed, evidence suggests that the general biological impoverishment within the urban context envisioned thirty years ago was overstated. Many of the world’s urban centers support some degree of biodiversity that is indigenous, as well as a complex array of non-native species, resulting in highly functional, and often, novel communities. For over two decades, a multi-disciplinary team has examined the sub-lethal impact of soil metal contamination on the multi-trophic biodiversity and ecosystem functioning of a post-industrial brownfield in the New York City metropolitan area. We do this through examinations of photosynthesis, carbon allocation, and soil enzyme activity as well as multi-trophic metal translocation via the plant and rhizosphere. In this paper, we synthesize the findings of our research network and apply the results to a framework of functional diversity. Due to the unique constraints many post-industrial lands impose on communities, functional diversity may be more meaningful to ecosystem health than species richness. Full article
(This article belongs to the Special Issue Food Webs, Ecosystem Functioning and Environmental Quality)
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Open AccessReview Ecophysiology of Amphibians: Information for Best Mechanistic Models
Diversity 2018, 10(4), 118; https://doi.org/10.3390/d10040118
Received: 1 August 2018 / Revised: 22 October 2018 / Accepted: 23 October 2018 / Published: 26 October 2018
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Abstract
Several amphibian lineages epitomize the faunal biodiversity crises, with numerous reports of population declines and extinctions worldwide. Predicting how such lineages will cope with environmental changes is an urgent challenge for biologists. A promising framework for this involves mechanistic modeling, which integrates organismal [...] Read more.
Several amphibian lineages epitomize the faunal biodiversity crises, with numerous reports of population declines and extinctions worldwide. Predicting how such lineages will cope with environmental changes is an urgent challenge for biologists. A promising framework for this involves mechanistic modeling, which integrates organismal ecophysiological features and ecological models as a means to establish causal and consequential relationships of species with their physical environment. Solid frameworks built for other tetrapods (e.g., lizards) have proved successful in this context, but its extension to amphibians requires care. First, the natural history of amphibians is distinct within tetrapods, for it includes a biphasic life cycle that undergoes major habitat transitions and changes in sensitivity to environmental factors. Second, the accumulated data on amphibian ecophysiology is not nearly as expressive, is heavily biased towards adult lifeforms of few non-tropical lineages, and overlook the importance of hydrothermal relationships. Thus, we argue that critical usage and improvement in the available data is essential for enhancing the power of mechanistic modeling from the physiological ecology of amphibians. We highlight the complexity of ecophysiological variables and the need for understanding the natural history of the group under study and indicate directions deemed crucial to attaining steady progress in this field. Full article
(This article belongs to the Special Issue Conservation and Ecology of Amphibians)
Open AccessArticle Biodiversity of Kelp Forests and Coralline Algae Habitats in Southwestern Greenland
Diversity 2018, 10(4), 117; https://doi.org/10.3390/d10040117
Received: 22 August 2018 / Revised: 21 October 2018 / Accepted: 22 October 2018 / Published: 25 October 2018
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Abstract
All marine communities in Greenland are experiencing rapid environmental change, and to understand the effects on those structured by seaweeds, baseline records are vital. The kelp and coralline algae habitats along Greenland’s coastlines are rarely studied, and we fill this knowledge gap for [...] Read more.
All marine communities in Greenland are experiencing rapid environmental change, and to understand the effects on those structured by seaweeds, baseline records are vital. The kelp and coralline algae habitats along Greenland’s coastlines are rarely studied, and we fill this knowledge gap for the area around Nuuk, west Greenland. Using subtidal swath surveys, photo-quadrats, and grab samples, we characterised the diversity of floral and faunal assemblages in kelp forests and coralline algae beds. The most abundant herbivore assemblages and the most diverse communities occur in the interstitial habitats of rhodolith beds. In kelp forests, species diversity is higher in epi-benthic (photo-quadrat) and mid-water (swath) surveys. These habitats are not mutually exclusive; Agarum clathratum is prominent in coralline algal habitats, while crustose coralline algae cover the bedrock under kelp holdfasts. Overall, the suite of surveys used capture the diverse communities within kelp forests and coralline algae in Greenland and their differing role in the life history of the inhabitants. Furthermore, coralline algae beds are an important carbonate store, with CaCO3 concentrations ranging from 28.06 to 103.73 g·m−3. Our research sets the baseline for continued investigations and monitoring of these important habitats and their supported fisheries. Full article
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Open AccessArticle Diversity of Curculionoidea in Humid Rain Forest Canopies of Borneo: A Taxonomic Blank Spot
Diversity 2018, 10(4), 116; https://doi.org/10.3390/d10040116
Received: 19 July 2018 / Revised: 17 October 2018 / Accepted: 18 October 2018 / Published: 23 October 2018
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Abstract
From 1992 to 2009, 334 trees were sampled by insecticidal knockdown on Borneo, Malaysia. Here, we describe the taxonomic composition of the 9671 specimens and 1589 species Curculionoidea collected (with additional notes on Cerambycidae). We found a largely unknown fauna with an assumed [...] Read more.
From 1992 to 2009, 334 trees were sampled by insecticidal knockdown on Borneo, Malaysia. Here, we describe the taxonomic composition of the 9671 specimens and 1589 species Curculionoidea collected (with additional notes on Cerambycidae). We found a largely unknown fauna with an assumed proportion of over 80% of species new to science, including all 33 Apionidae and 26 Ceutorhynchinae species. Specialists could usually identify only a few specimens leaving the remaining beetles for further investigation. The samples contain numerous genera, two tribes (Egriini, Viticiini), one subfamily (Mesoptiliinae) and one family (Belidae) new to Borneo and several genera not recorded west of the Wallace line before. These data show how little is known about canopy diversity. The lack of taxonomic knowledge implies a respective lack of autecological knowledge and is alarming. Some taxa differed conspicuously between primary and disturbed forests. In contrast to common literature, our results let us conclude that current efforts to narrow down the extent of tropical diversity and its ecological importance must consider the enormous species diversity of the canopy. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessCommunication Response of Seagrass ‘Blue Carbon’ Stocks to Increased Water Temperatures
Diversity 2018, 10(4), 115; https://doi.org/10.3390/d10040115
Received: 27 August 2018 / Revised: 16 October 2018 / Accepted: 19 October 2018 / Published: 22 October 2018
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Abstract
Seagrass meadows are globally important sinks of ‘Blue Carbon’, but warming water temperatures due to climate change may undermine their capacity to sequester and retain organic carbon (Corg). We tested the effects of warming on seagrass Corg stocks in situ by transplanting seagrass [...] Read more.
Seagrass meadows are globally important sinks of ‘Blue Carbon’, but warming water temperatures due to climate change may undermine their capacity to sequester and retain organic carbon (Corg). We tested the effects of warming on seagrass Corg stocks in situ by transplanting seagrass soil cores along a thermal plume generated by a coal-fired power plant in a seagrass-dominated estuary (Lake Macquarie, Australia). Transplanted cores were subjected to temperatures 2 and 4 °C above ambient temperatures and Corg content was measured after 7, 30, 90 and 180 days. We were unable to detect any significant effect of warming on Corg concentration, stocks, chemical composition (as measured by labile, recalcitrant, refractory ratios), or microbial abundance at any time point. In fact, Corg levels were temporally variable. These findings contrast those of previous studies (mostly laboratory-based) that have reported increases in microbial remineralisation (breakdown) of Corg in response to warming. To explain the lack of any detectable warming effect, we suggest that higher temperatures, longer durations of warming exposure, or additional stressors (e.g., oxygen exposure) may be needed to overcome microbial activation barriers and stimulate Corg remineralisation. Full article
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Open AccessArticle Sequence Diversity and Identification of Novel Puroindoline and Grain Softness Protein Alleles in Elymus, Agropyron and Related Species
Diversity 2018, 10(4), 114; https://doi.org/10.3390/d10040114
Received: 12 September 2018 / Revised: 8 October 2018 / Accepted: 11 October 2018 / Published: 18 October 2018
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Abstract
The puroindoline proteins, PINA and PINB, which are encoded by the Pina and Pinb genes located at the Ha locus on chromosome 5D of bread wheat, are considered to be the most important determinants of grain hardness. However, the recent identification of Pinb-2 [...] Read more.
The puroindoline proteins, PINA and PINB, which are encoded by the Pina and Pinb genes located at the Ha locus on chromosome 5D of bread wheat, are considered to be the most important determinants of grain hardness. However, the recent identification of Pinb-2 genes on group 7 chromosomes has stressed the importance of considering the effects of related genes and proteins. Several species related to wheat (two diploid Agropyron spp., four tetraploid Elymus spp. and five hexaploid Elymus and Agropyron spp.) were therefore analyzed to identify novel variation in Pina, Pinb and Pinb-2 genes which could be exploited for the improvement of cultivated wheat. A novel sequence for the Pina gene was detected in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus and Elymus nutans and novel PINB sequences in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus, and Elymus nutans. A novel PINB-2 variant was also detected in Agropyron repens and Elymus repens. The encoded proteins detected all showed changes in the tryptophan-rich domain as well as changes in and/or deletions of basic and hydrophobic residues. In addition, two new AGP sequences were identified in Elymus nutans and Elymus wawawaiensis. The data presented therefore highlight the sequence diversity in this important gene family and the potential to exploit this diversity to modify grain texture and end-use quality in wheat. Full article
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Open AccessArticle Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation
Diversity 2018, 10(4), 113; https://doi.org/10.3390/d10040113
Received: 29 August 2018 / Revised: 25 September 2018 / Accepted: 29 September 2018 / Published: 18 October 2018
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Abstract
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can [...] Read more.
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals. Full article
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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Open AccessArticle Distribution of Cranberry Blue Butterflies (Agriades optilete) and Their Responses to Forest Disturbance from In Situ Oil Sands and Wildfires
Diversity 2018, 10(4), 112; https://doi.org/10.3390/d10040112
Received: 26 September 2018 / Revised: 15 October 2018 / Accepted: 15 October 2018 / Published: 17 October 2018
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Abstract
Cranberry blues (Agriades optilete) are butterflies of conservation interest worldwide. Less than 20 populations are known in Alberta, Canada, mostly inhabiting boreal forests that are increasingly fragmented by oil sands developments and subject to wildfires. We modeled the abundance of cranberry [...] Read more.
Cranberry blues (Agriades optilete) are butterflies of conservation interest worldwide. Less than 20 populations are known in Alberta, Canada, mostly inhabiting boreal forests that are increasingly fragmented by oil sands developments and subject to wildfires. We modeled the abundance of cranberry blues in the boreal forests of Alberta’s Wood Buffalo Region as a function of forest characteristics, presence of disturbances associated with in situ oil sands exploration, and wildfire disturbance, while accounting for butterfly detectability as a function of sampling conditions. We counted 188 cranberry blues during 1280 samples, discovering 14 unknown populations using a species distribution model based on forest wetness and canopy height. Probability of detection peaked around 5th July, and at higher temperatures and in the absence of wind, with cranberry blues preferring wetter treed peatland forests with low canopy heights. Seismic lines were positively related to the abundance of cranberry blues (400% increase), while exploratory well pads and wildfires were negatively related (60% and 90% loss, respectively). Overall, cranberry blue populations are small and locally sensitive to both natural and anthropogenic disturbances. Despite a narrow habitat specificity, cranberry blues seem more widely distributed than previously thought in northern Alberta (57% of the study area deemed suitable). Full article
(This article belongs to the Special Issue Butterfly Conservation)
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Open AccessArticle DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)
Diversity 2018, 10(4), 111; https://doi.org/10.3390/d10040111
Received: 29 August 2018 / Revised: 10 October 2018 / Accepted: 10 October 2018 / Published: 15 October 2018
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Abstract
DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on [...] Read more.
DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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Open AccessArticle The Variable Influences of Sea Level, Sedimentation and Exposure on Holocene Reef Development over a Cross-Shelf Transect, Central Great Barrier Reef
Diversity 2018, 10(4), 110; https://doi.org/10.3390/d10040110
Received: 5 August 2018 / Revised: 25 September 2018 / Accepted: 4 October 2018 / Published: 11 October 2018
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Abstract
Coral reefs globally are impacted by natural and anthropogenic stressors that are compounded by climate change. Understanding past reef responses to natural stressors (cyclones, sea-level change, freshwater inputs, and sedimentation) can provide important insights to further understand recent (within the past century) trends [...] Read more.
Coral reefs globally are impacted by natural and anthropogenic stressors that are compounded by climate change. Understanding past reef responses to natural stressors (cyclones, sea-level change, freshwater inputs, and sedimentation) can provide important insights to further understand recent (within the past century) trends in coral cover and diversity. Here we use a compilation of recently published data to investigate the Holocene development of five fringing reefs that are located on a cross-shelf transect on the central Great Barrier Reef, and that are exposed to varying degrees of natural and anthropogenic sedimentation, storm exposure, and Holocene sea-level change. Forty-two reef cores collected using a combination of manual percussion coring and hydraulic drilling techniques, were analysed and dated using uranium-thorium methods. The chronostratigraphic records of reef development established using 105 recently published radiometric ages and seven new uranium-thorium ages from the reef cores and fossil microatolls preserved across the reef flats were compared to investigate cross-shelf variations in reef development. This is the first study to conduct an internal investigation of reef framework across an inshore–offshore gradient to examine the varying levels of influence of sedimentation, sea level and cyclones. Our observations from the central Great Barrier Reef show that reefs furthest offshore from the mainland coast were typically initiated earliest after the post-glacial marine transgression. Reef flat size, morphology, and growth style varied according to constraints placed on reef development by the composition, depth, shape, and relief of the underlying substrate. We establish that terrigenous sedimentation had a marked effect on the development of inshore reefs closest to the mainland (within 10 km of the mainland coast). Periods of relatively high terrigenous sedimentation correspond with enhanced reef accretion rates, and also resulted in a superior record of palaeo-ecological coral composition (i.e., better preservation) at inshore sites. In contrast, mid-Holocene cyclones played a seemingly more important role in the development of reefs >10 km from the mainland; although cyclones clearly affect reefs closer inshore, their geomorphology is affected by a range of controlling factors. Insights provided by these five Holocene reef chronostratigraphies provide useful baseline understanding of reef condition and growth along a cross-shelf transect where the reefs are exposed to variable stressors. Full article
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Open AccessReview Recovering Plant Data for Guinea-Bissau: Implications for Biodiversity Knowledge of West Africa
Diversity 2018, 10(4), 109; https://doi.org/10.3390/d10040109
Received: 10 September 2018 / Revised: 29 September 2018 / Accepted: 1 October 2018 / Published: 6 October 2018
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Abstract
The rich plant diversity that characterizes the West African Region and the inherent knowledge of their flora and vegetation has been the backbone of scientific explorations during the past centuries. The evolution of botanical knowledge on Guinea-Bissau, throughout the 16th and 20th centuries [...] Read more.
The rich plant diversity that characterizes the West African Region and the inherent knowledge of their flora and vegetation has been the backbone of scientific explorations during the past centuries. The evolution of botanical knowledge on Guinea-Bissau, throughout the 16th and 20th centuries is reviewed. We present and discuss floristic data collected by scientific expeditions between the mid-1700s to 1974, when the Portuguese colonial period ended. Expeditions undertaken by French naturalists provided some of the earliest plant collections. A list of herbarium specimens collected by the French naturalist Jardin, in the Bijagós Islands in ca. 1847–1858 is presented here for the first time, while in the late 1800s some Portuguese naturalists also explored Guinea-Bissau. During the colonial period (1915–1974), Gomes e Sousa published the first comprehensive study of the territory’s flora while Espírito Santo assembled the largest plant collection. Our review applies a multi-disciplinary perspective to fill important lacuna regarding biodiversity knowledge of this under-researched West African country. It constitutes the first study tracing the long term evolution of knowledge on Guinea Bissau's plant diversity, which provides the basis for understanding trends and research priorities, in particular in conservation and botanical fields. Full article
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Open AccessArticle Reconnecting Amphibian Habitat through Small Pond Construction and Enhancement, South Okanagan River Valley, British Columbia, Canada
Diversity 2018, 10(4), 108; https://doi.org/10.3390/d10040108
Received: 31 May 2018 / Revised: 6 September 2018 / Accepted: 7 September 2018 / Published: 29 September 2018
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Abstract
The arid south Okanagan River Valley, British Columbia is a highly-modified landscape; where wetland and riparian habitat loss exceeds 85%, and 88% of remaining wetlands experience at least one harmful anthropogenic stressor. This multi-stressor landscape for amphibian species at risk led to a [...] Read more.
The arid south Okanagan River Valley, British Columbia is a highly-modified landscape; where wetland and riparian habitat loss exceeds 85%, and 88% of remaining wetlands experience at least one harmful anthropogenic stressor. This multi-stressor landscape for amphibian species at risk led to a collaborative stakeholder approach for habitat restoration and species recovery. The main project goal was to increase the quantity and quality of lowland wetland habitat by reconnecting known amphibian-breeding sites with constructed and/or enhanced small ponds. Long-term amphibian monitoring data were used to determine strategic locations for wetland construction and/or enhancement. Habitat enhancement outcomes (Ntotal = 21 sites) since 2006 include 10 newly constructed ponds, enhancement of eight re-contoured ponds after historic infilling, and invasive predatory species removal at three sites. Project ponds were monitored annually (2007 to 2014) for calling frogs, the presence of eggs, and metamorphic emergence. Early signs of colonization and metamorphic success for Great Basin Spadefoot (Spea intermontana) (N = 13 sites) and Pacific treefrog (Pseudacris regilla) (N = 7 sites) populations have been observed, however no records of Blotched tiger salamanders (Ambystoma mavortium) colonization has been detected. Wetland habitat construction and enhancement have doubled the number of available fishless ponds to support breeding within the study area and engaged landowners through voluntary stewardship. Whether constructed or enhanced ponds have aided species recovery is unclear, though the colonization and successful metamorphosis of some species provides early supporting evidence that it will. Full article
(This article belongs to the Special Issue Conservation and Ecology of Amphibians)
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Open AccessArticle First Record of Juncaceicola as Endophytic Fungi Associated with Deschampsia antarctica Desv.
Diversity 2018, 10(4), 107; https://doi.org/10.3390/d10040107
Received: 13 April 2018 / Revised: 20 July 2018 / Accepted: 31 July 2018 / Published: 27 September 2018
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Abstract
In the current study, we present the molecular characterization of an endophyte fungus associated with the leaves of Deschampsia antarctica Desv. (Poaceae), a monocot species native to Antarctica. The isolate was obtained from 90 leaf fragments from two distinct collection sites, both located [...] Read more.
In the current study, we present the molecular characterization of an endophyte fungus associated with the leaves of Deschampsia antarctica Desv. (Poaceae), a monocot species native to Antarctica. The isolate was obtained from 90 leaf fragments from two distinct collection sites, both located on Half Moon Island, South Shetland Islands and Maritime Antarctica. The internal transcribed spacer region (ITS) was sequenced and the endophytic fungus was identified as belonging to the genus Juncaceicola Tennakoon, Camporesi, Phook and K.D. Hyde (99% nucleotide sequence identity). When compared to all fungi of the genus Juncaceicola deposited in data base, our isolate showed greater proximity with Juncaceicola typharum, however, because it presents a low bootstrap value to be considered a new species, we treat it as Juncaceicola cf. typharum. Moreover, the identification of our isolate as belonging to the genus Juncaceicola makes this the first occurrence of a species of this genus to be associated with the leaves of Antarctic plants. This work is considered as a starting point for other studies with fungi of this genus associated with leaves of Deschampsia antarctica, as it presents results from two collection points on a single Antarctic island, suggesting that new sites and new Antarctic islands should be explored. Full article
(This article belongs to the Special Issue Climate Change Impacts on Alpine and Polar Plants)
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Open AccessArticle Relationship between Genetic Variability and Land Use and Land Cover in Populations of Campomanesia adamantium (Myrtaceae)
Diversity 2018, 10(4), 106; https://doi.org/10.3390/d10040106
Received: 30 May 2018 / Revised: 1 July 2018 / Accepted: 15 July 2018 / Published: 27 September 2018
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Abstract
Campomanesia adamantium is an endemic plant of Cerrado biome that has potential for cultivation because its fruits have culinary and medicinal uses. However, genetic diversity studies using molecular markers with Cerrado species are scarce, and the inadequate extractive exploitation of fruits and the [...] Read more.
Campomanesia adamantium is an endemic plant of Cerrado biome that has potential for cultivation because its fruits have culinary and medicinal uses. However, genetic diversity studies using molecular markers with Cerrado species are scarce, and the inadequate extractive exploitation of fruits and the expansion of agricultural frontiers may also affect genetic variability. Therefore, studies in this field are of interest as they can provide sources for conservation and breeding programs. In this context, we investigated the genetic diversity of native populations of C. adamantium from different sites and the relationship between genetic variability and the land use and land cover of each site. A total of 207 plants were sampled in seven sites and characterized with seven polymorphic microsatellite markers. The use and coverage of land were mapped based on aerial images, and the land was classified into different categories. The genetic diversity was high in all populations, with low levels of differentiation due to allele sharing, mainly in Mato Grosso do Sul and Paraguay populations. The geographically closest populations were more genetically similar. The use and coverage of land indicated that intense agriculture promotes a significant decrease in genetic variability. Full article
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Open AccessArticle Winter Roost Tree Selection and Phenology of the Long-Eared Owl (Asio otus) in Crimea
Diversity 2018, 10(4), 105; https://doi.org/10.3390/d10040105
Received: 23 August 2018 / Revised: 19 September 2018 / Accepted: 22 September 2018 / Published: 27 September 2018
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Abstract
The winter roost of the long-eared owl Asio otus in Crimea (South of Ukraine), located in Simferopol, is described. In 2015–2017, the number of long-eared owls varied on a convex curve, with the maximum reached at the end of November and in December. [...] Read more.
The winter roost of the long-eared owl Asio otus in Crimea (South of Ukraine), located in Simferopol, is described. In 2015–2017, the number of long-eared owls varied on a convex curve, with the maximum reached at the end of November and in December. The birds exhibited a strong preference for roosting in conifers, where we recorded 89% of the owls. There was an inverse relationship between the mean of the maximum daily temperature (°C) and the number of owls in both seasons. The owls were not sensitive to abrupt but short-term temperature changes, but the temperature decrease curve caused practically synchronous changes in the dynamics of bird numbers. It was found that the number of owls significantly differed based on weather conditions in 16 trees. The proportion of owls sitting on coniferous trees increased with unfavourable weather, and the converse pattern was observed for deciduous trees. Full article
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Open AccessArticle Seasonal Use of Railways by Wildlife
Diversity 2018, 10(4), 104; https://doi.org/10.3390/d10040104
Received: 26 July 2018 / Revised: 10 September 2018 / Accepted: 18 September 2018 / Published: 25 September 2018
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Abstract
Despite the rapid advancements in the field of road ecology, very little research has been done in railway ecology. Basic research, such as railway use by wildlife, is relatively undocumented, albeit very important in understanding the potential negative and positive effects of railways [...] Read more.
Despite the rapid advancements in the field of road ecology, very little research has been done in railway ecology. Basic research, such as railway use by wildlife, is relatively undocumented, albeit very important in understanding the potential negative and positive effects of railways on wildlife and ecosystems. We provide one of the first studies documenting wildlife railway use using motion-triggered cameras along a 20 km stretch of railway in Ontario. Our objectives were to develop a much-needed baseline understanding of railway use by endemic wildlife species, investigate differences in frequency of use among species, compare diurnal versus nocturnal use, and determine if railway use by wildlife was uniform or spatially varied. We found a significant proportion of medium-to-large resident mammalian fauna and several avian species non-uniformly using the studied railway. Some species used the railway as a travel corridor, while others appeared to use it incidentally. Diel and seasonal patterns of use were apparent for many species. Our findings emphasize the importance of species-specific investigations of railway ecology. The collection of baseline information on railway use by wildlife is critical in view of the dearth of available data, and we highly encourage further research in all aspects of wildlife–railway ecology. Full article
(This article belongs to the Special Issue Impacts of Linear Infrastructures on Wildlife)
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