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Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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15 pages, 1822 KiB  
Article
Digging Deeper into the Ecology of Subterranean Ants: Diversity and Niche Partitioning across Two Continents
by Mickal Houadria and Florian Menzel
Diversity 2021, 13(2), 53; https://doi.org/10.3390/d13020053 - 29 Jan 2021
Cited by 4 | Viewed by 3308
Abstract
Soil fauna is generally understudied compared to above-ground arthropods, and ants are no exception. Here, we compared a primary and a secondary forest each on two continents using four different sampling methods. Winkler sampling, pitfalls, and four types of above- and below-ground baits [...] Read more.
Soil fauna is generally understudied compared to above-ground arthropods, and ants are no exception. Here, we compared a primary and a secondary forest each on two continents using four different sampling methods. Winkler sampling, pitfalls, and four types of above- and below-ground baits (dead, crushed insects; melezitose; living termites; living mealworms/grasshoppers) were applied on four plots (4 × 4 grid points) on each site. Although less diverse than Winkler samples and pitfalls, subterranean baits provided a remarkable ant community. Our baiting system provided a large dataset to systematically quantify strata and dietary specialisation in tropical rainforest ants. Compared to above-ground baits, 10–28% of the species at subterranean baits were overall more common (or unique to) below ground, indicating a fauna that was truly specialised to this stratum. Species turnover was particularly high in the primary forests, both concerning above-ground and subterranean baits and between grid points within a site. This suggests that secondary forests are more impoverished, especially concerning their subterranean fauna. Although subterranean ants rarely displayed specific preferences for a bait type, they were in general more specialised than above-ground ants; this was true for entire communities, but also for the same species if they foraged in both strata. Full article
(This article belongs to the Special Issue Diversity, Biogeography and Community Ecology of Ants)
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15 pages, 2571 KiB  
Review
How Many Sipunculan Species Are Hiding in Our Oceans?
by Anja Schulze and Gisele Y. Kawauchi
Diversity 2021, 13(2), 43; https://doi.org/10.3390/d13020043 - 24 Jan 2021
Cited by 20 | Viewed by 10837
Abstract
Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they [...] Read more.
Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they have no chaetae, but the introvert is often adorned with proteinaceous hooks that can be important taxonomic characters. Other external taxonomic characters include the tentacles (number, shape and arrangement), body papillae and, in some cases, hardened shields, as well as length ratios. Many species require dissection for correct identification to reveal internal characteristics, such as introvert retractor muscles, nephridia and contractile vessels. Here we summarize the state of the current knowledge of species diversity in sipunculans. We emphasize molecular studies, conducted over the past two decades, that have revealed multiple complexes of cryptic or pseudocryptic species. It has become obvious that diversity is significantly higher than the current taxonomic scheme accounts for, but formal species descriptions are lagging behind. Although the major branches in the sipunculan phylogeny have become increasingly consolidated, the internal relationships within most branches are still in flux. Full article
(This article belongs to the Special Issue Systematics and Diversity of Annelids)
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44 pages, 17099 KiB  
Review
On the Systematics and Biodiversity of the Palaeoannelida
by Julio Parapar, Kate Mortimer, María Capa and Juan Moreira
Diversity 2021, 13(2), 41; https://doi.org/10.3390/d13020041 - 21 Jan 2021
Cited by 12 | Viewed by 5866
Abstract
Palaeoannelida Weigert and Bleidorn, 2016 is an old clade branching off at the base of the Annelida radiation. It includes two morphologically and ecological divergent groups of sedentary burrowers and tube-dwellers: Magelonidae Cunningham and Ramage, 1888, and Oweniidae Rioja, 1917. Magelonids are characterised [...] Read more.
Palaeoannelida Weigert and Bleidorn, 2016 is an old clade branching off at the base of the Annelida radiation. It includes two morphologically and ecological divergent groups of sedentary burrowers and tube-dwellers: Magelonidae Cunningham and Ramage, 1888, and Oweniidae Rioja, 1917. Magelonids are characterised by a flattened, shovel-shaped prostomium and a pair of ventral papillated palps. Oweniids have simplified bodies lacking parapodia or appendages and are easily distinguished by the presence of oval patches of packed uncini, each with two distal curved teeth. The present review aims to summarise available information about the diversity of forms and life strategies displayed in the group, providing some guidelines for species identification and the techniques commonly used for their study. In addition, the assumed geographic distributions of some taxa are critically discussed. A brief introduction about the evolutionary relationships, systematics, and taxonomic history is given for both Magelonidae and Oweniidae. The motivation of this review is to highlight the main knowledge gaps from a taxonomic, methodological, and geographic perspective, aiming at stimulating further research into members of this clade. Full article
(This article belongs to the Special Issue Systematics and Diversity of Annelids)
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13 pages, 549 KiB  
Review
Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview
by Svante Martinsson and Christer Erséus
Diversity 2021, 13(2), 36; https://doi.org/10.3390/d13020036 - 20 Jan 2021
Cited by 25 | Viewed by 5822
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also [...] Read more.
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field. Full article
(This article belongs to the Special Issue Systematics and Diversity of Annelids)
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12 pages, 2375 KiB  
Article
Occupancy of the American Three-Toed Woodpecker in a Heavily-Managed Boreal Forest of Eastern Canada
by Vincent Lamarre and Junior A. Tremblay
Diversity 2021, 13(1), 35; https://doi.org/10.3390/d13010035 - 19 Jan 2021
Cited by 7 | Viewed by 3348
Abstract
The southern extent of the boreal forest in North America has experienced intensive human disturbance in recent decades. Among these, forest harvesting leads to the substantial loss of late-successional stands that include key habitat attributes for several avian species. The American Three-toed Woodpecker, [...] Read more.
The southern extent of the boreal forest in North America has experienced intensive human disturbance in recent decades. Among these, forest harvesting leads to the substantial loss of late-successional stands that include key habitat attributes for several avian species. The American Three-toed Woodpecker, Picoides dorsalis, is associated with continuous old spruce forests in the eastern part of its range. In this study, we assessed the influence of habitat characteristics at different scales on the occupancy of American Three-toed Woodpecker in a heavily-managed boreal landscape of northeastern Canada, and we inferred species occupancy at the regional scale. We conducted 185 playback stations over two breeding seasons and modelled the occupancy of the species while taking into account the probability of detection. American Three-toed Woodpecker occupancy was lower in stands with large areas recently clear-cut, and higher in landscapes with large extents of old-growth forest dominated by black spruce. At the regional scale, areas with high probability of occupancy were scarce and mostly within protected areas. Habitat requirements of the American Three-toed Woodpecker during the breeding season, coupled with overall low occupancy rate in our study area, challenge its long-term sustainability in such heavily managed landscapes. Additionally, the scarcity of areas of high probability of occupancy in the region suggests that the ecological role of old forest outside protected areas could be compromised. Full article
(This article belongs to the Special Issue Boreal Bird Ecology, Management and Conservation)
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16 pages, 2582 KiB  
Article
Threats Posed to the Rediscovered and Rare Salvia ceratophylloides Ard. (Lamiaceae) by Borer and Seed Feeder Insect Species
by Carmelo Peter Bonsignore, Valentina Lucia Astrid Laface, Gregorio Vono, Rita Marullo, Carmelo Maria Musarella and Giovanni Spampinato
Diversity 2021, 13(1), 33; https://doi.org/10.3390/d13010033 - 16 Jan 2021
Cited by 19 | Viewed by 4348
Abstract
The effects of herbivorous insects on a plant population are not always well tolerated. This is especially true if the herbivorous actions are directed toward rare plant species. Salvia ceratophylloides Ard. is a rare endemism of southern Italy. Observations of the plants in [...] Read more.
The effects of herbivorous insects on a plant population are not always well tolerated. This is especially true if the herbivorous actions are directed toward rare plant species. Salvia ceratophylloides Ard. is a rare endemism of southern Italy. Observations of the plants in situ revealed that many of them were under severe stress and did not produce seeds. Therefore, to find out which factors affect the reproductive activity as a whole, an observational study was carried out. We found bottom-up and top-down effects on plant health and reproduction associated with herbivorous action. Squamapion elongatum (Coleoptera, Curculionoidea, Apionidae), in all monitored sites, infested plants non-uniformly but was able to threaten the health condition, flowering, and seed production of sage by digging tunnels into the sage branches (bottom-up action), and then secondarily by seed feeder Systole salvia Zerova (Hymenoptera, Eurytomidae) predating sage seeds (top-down action). Mainly, chalcid parasitoid wasps such as Trichomalus spp. (Hymenoptera, Pteromalidae), as well as Eupelmus vesicularis and E. muellneri (Hymenoptera, Eupelmidae), limited the herbivorous S. elongatum population and the seed herbivore S. salviae emerged with its parasitoid Ormyrus diffinis (Hymenoptera, Ormyridae). Overall, this study showed how ecological interactions among herbivores, their host, and their natural enemies act on this sage species in all sites investigated. Among the herbivores, mainly S. elongatum affected this rare sage species, which should be taken into consideration, especially in the formulation of biological control solutions and for improving operating practice aimed at reproducing the species. This study provides the molecular characterization of the herbivorous species involved, in order to support future projects to evaluate the intra- and interspecific genetic variability of insects, their evolutionary relationships, and phylogeny studies. Full article
(This article belongs to the Special Issue Biodiversity of Insect)
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14 pages, 1988 KiB  
Review
The Role of Carrion in the Landscapes of Fear and Disgust: A Review and Prospects
by Marcos Moleón and José A. Sánchez-Zapata
Diversity 2021, 13(1), 28; https://doi.org/10.3390/d13010028 - 13 Jan 2021
Cited by 29 | Viewed by 5289
Abstract
Animal behavior is greatly shaped by the ‘landscape of fear’, induced by predation risk, and the equivalent ‘landscape of disgust’, induced by parasitism or infection risk. However, the role that carrion may play in these landscapes of peril has been largely overlooked. Here, [...] Read more.
Animal behavior is greatly shaped by the ‘landscape of fear’, induced by predation risk, and the equivalent ‘landscape of disgust’, induced by parasitism or infection risk. However, the role that carrion may play in these landscapes of peril has been largely overlooked. Here, we aim to emphasize that animal carcasses likely represent ubiquitous hotspots for both predation and infection risk, thus being an outstanding paradigm of how predation and parasitism pressures can concur in space and time. By conducting a literature review, we highlight the manifold inter- and intra-specific interactions linked to carrion via predation and parasitism risks, which may affect not only scavengers, but also non-scavengers. However, we identified major knowledge gaps, as reviewed articles were highly biased towards fear, terrestrial environments, vertebrates, and behavioral responses. Based on the reviewed literature, we provide a conceptual framework on the main fear- and disgust-based interaction pathways associated with carrion resources. This framework may be used to formulate predictions about how the landscape of fear and disgust around carcasses might influence animals’ individual behavior and ecological processes, from population to ecosystem functioning. We encourage ecologists, evolutionary biologists, epidemiologists, forensic scientists, and conservation biologists to explore the promising research avenues associated with the scary and disgusting facets of carrion. Acknowledging the multiple trophic and non-trophic interactions among dead and live animals, including both herbivores and carnivores, will notably improve our understanding of the overlapping pressures that shape the landscape of fear and disgust. Full article
(This article belongs to the Special Issue Ecology of Predation and Scavenging and the Interface)
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31 pages, 18530 KiB  
Review
The Early Branching Group of Orbiniida Sensu Struck et al., 2015: Parergodrilidae and Orbiniidae
by Miguel A. Meca, Anna Zhadan and Torsten H. Struck
Diversity 2021, 13(1), 29; https://doi.org/10.3390/d13010029 - 13 Jan 2021
Cited by 9 | Viewed by 4921
Abstract
This review addresses the state of the art of the systematics and the improvements in the biology, ecology and species diversity of the two annelid taxa Parergodrilidae and Orbiniidae, the early branching group of Orbiniida sensu Struck et al., 2015 according to molecular [...] Read more.
This review addresses the state of the art of the systematics and the improvements in the biology, ecology and species diversity of the two annelid taxa Parergodrilidae and Orbiniidae, the early branching group of Orbiniida sensu Struck et al., 2015 according to molecular studies. An effort to identify gaps of knowledge is given to understand the distribution, dispersal and the diversity Parergodrilidae and Orbiniidae hold, as well as to give several directions for future research. Parergodrilidae is a taxon of interstitial annelids constituted by the terrestrial Parergodrilus heideri (monotypic genus up to date), reported throughout Europe but also in Korea and North America, and the genus Stygocapitella, which includes eleven species from the upper shore of sandy beaches distributed along Europe and other regions of the world. Orbiniidae contains more than 200 described species spread over 20 valid genera, varying in size from a few millimeters up to 30 cm, distributed globally and living in a wide variety of soft bottoms. Improving the knowledge on these two sister-taxa is crucial for the understanding of the evolution to interstitial forms by progenesis in Annelida. Full article
(This article belongs to the Special Issue Systematics and Diversity of Annelids)
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11 pages, 894 KiB  
Review
Reduced Oxygen as an Environmental Pressure in the Evolution of the Blind Mexican Cavefish
by Tyler Boggs and Joshua Gross
Diversity 2021, 13(1), 26; https://doi.org/10.3390/d13010026 - 12 Jan 2021
Cited by 18 | Viewed by 4818
Abstract
Extreme environmental features can drive the evolution of extreme phenotypes. Over the course of evolution, certain environmental changes may be so drastic that they lead to extinction. Conversely, if an organism adapts to harsh environmental changes, the adaptations may permit expansion of a [...] Read more.
Extreme environmental features can drive the evolution of extreme phenotypes. Over the course of evolution, certain environmental changes may be so drastic that they lead to extinction. Conversely, if an organism adapts to harsh environmental changes, the adaptations may permit expansion of a novel niche. The interaction between environmental stressors and adaptive changes is well-illustrated by the blind Mexican cavefish, Astyanaxmexicanus, which has recurrently adapted to the stark subterranean environment. The transition from terrestrial rivers and streams (occupied by extant surface morphs of the same species) to the cave has been accompanied by the resorption of eyes, diminished pigmentation and reduced metabolism in cave-dwelling morphs. The principal features of caves most often associated with evolution of these common cave features are the absence of light and limited nutrition. However, a putatively essential cave feature that has received less attention is the frequently low concentration of oxygen within natural karst environments. Here, we review the potential role of limited oxygen as a critical environmental feature of caves in the Sierra de El Abra. Additionally, we review evidence that Astyanax cavefish may have evolved adaptive features enabling them to thrive in lower oxygen compared to their surface-dwelling counterparts. Full article
(This article belongs to the Special Issue Cave Communities: From the Surface Border to the Deep Darkness)
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13 pages, 1917 KiB  
Article
Parrot Ownership and Capture in Coastal Ecuador: Developing a Trapping Pressure Index
by Rebecca Biddle, Ivette Solis-Ponce, Martin Jones, Mark Pilgrim and Stuart Marsden
Diversity 2021, 13(1), 15; https://doi.org/10.3390/d13010015 - 5 Jan 2021
Cited by 8 | Viewed by 5817
Abstract
We located rural communities with pet parrots and used these locations to predict the probability of illegal parrot ownership across coastal Ecuador, using variables related to demand for pets, parrot availability, and trapping accessibility. In 12 pet keeping communities, we carried out in-depth [...] Read more.
We located rural communities with pet parrots and used these locations to predict the probability of illegal parrot ownership across coastal Ecuador, using variables related to demand for pets, parrot availability, and trapping accessibility. In 12 pet keeping communities, we carried out in-depth interviews with 106 people, to quantify ownership, trapping, and interviewees’ attitudes towards these behaviours. We combined these data to calculate a trapping pressure index for four key roosting, feeding and nesting sites for the Critically Endangered Lilacine or Ecuadorian Amazon Parrot Amazona lilacina. We found that 66% of all communities had pet parrots and 31% had pet Lilacines. Our predictive models showed that pet parrot ownership occurs throughout coastal Ecuador, but ownership of Lilacines by rural communities, is more likely to occur within the natural distribution of the species. The number of people per community who had owned Lilacines in the last three years varied from 0–50%, as did the number of people who had trapped them—from 0–26%. We interviewed 10 people who had captured the species in the last three years who reported motives of either to sell or keep birds as pets. Attitudes towards pet keeping and trapping differed among the 12 communities: 20–52% believed it was acceptable to keep pet parrots, and for 32–74%, it was acceptable to catch parrots to sell. This being said, most people believed that wild parrots were important for nature and that local people had a responsibility to protect them. We conclude that trapping pressure is greatest in the southern part of the Lilacine’s range, and urgent conservation measures such as nest and roost protection, and local community engagement are needed. Full article
(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)
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13 pages, 7883 KiB  
Article
Change of Ellipsoid Biovolume (EV) of Ground Beetles (Coleoptera, Carabidae) along an Urban–Suburban–Rural Gradient of Central Slovakia
by Vladimír Langraf, Stanislav David, Ramona Babosová, Kornélia Petrovičová and Janka Schlarmannová
Diversity 2020, 12(12), 475; https://doi.org/10.3390/d12120475 - 14 Dec 2020
Cited by 14 | Viewed by 2915
Abstract
Changes in the structure of ground beetle communities indicate environmental stability or instability influenced by, e.g., urbanization, agriculture, and forestry. It can affect flight capability and ellipsoid biovolume (EV) of ground beetles. Therefore, we analyzed ground beetles in various habitats. In the course [...] Read more.
Changes in the structure of ground beetle communities indicate environmental stability or instability influenced by, e.g., urbanization, agriculture, and forestry. It can affect flight capability and ellipsoid biovolume (EV) of ground beetles. Therefore, we analyzed ground beetles in various habitats. In the course of the period from 2015 to 2017, we recorded in pitfall traps 2379 individuals (1030 males and 1349 females) belonging to 52 species at six localities (two rural, two suburban, two urban). We observed the decrease in the average EV value and morphometric characters (length, height, and width of the body) of ground beetles in the direction of the rural–suburban–urban gradient. Our results also suggest a decrease in EV of apterous and brachypterous species and an increase in macropterous species in the urban and suburban landscapes near agricultural fields. The increasing EV of apterous and brachypterous species and the decreasing of macropterous species was observed in rural landscape conditions with not continuous cover forestry and partial forest management. The creation of habitat fragments in urbanized conditions is key to maintaining the average EV in apterous and brachypterous species in urban and suburban landscapes. Full article
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12 pages, 1289 KiB  
Article
The Evolution and Biogeography of Wolbachia in Ants (Hymenoptera: Formicidae)
by Manuela O. Ramalho and Corrie S. Moreau
Diversity 2020, 12(11), 426; https://doi.org/10.3390/d12110426 - 12 Nov 2020
Cited by 14 | Viewed by 6687
Abstract
Wolbachia bacteria are widely distributed across invertebrate taxa, including ants, but several aspects of this host-associated interaction are still poorly explored, especially with regard to the ancestral state association, origin, and dispersion patterns of this bacterium. Therefore, in this study, we explored the [...] Read more.
Wolbachia bacteria are widely distributed across invertebrate taxa, including ants, but several aspects of this host-associated interaction are still poorly explored, especially with regard to the ancestral state association, origin, and dispersion patterns of this bacterium. Therefore, in this study, we explored the association of Wolbachia with Formicidae in an evolutionary context. Our data suggest that supergroup F is the ancestral character state for Wolbachia infection in ants, and there is only one transition to supergroup A, and once ants acquired infection with supergroup A, there have been no other strains introduced. Our data also reveal that the origin of Wolbachia in ants likely originated in Asia and spread to the Americas, and then back to Asia. Understanding the processes and mechanisms of dispersion of these bacteria in Formicidae is a crucial step to advance the knowledge of this symbiosis and their implications in an evolutionary context. Full article
(This article belongs to the Special Issue Diversity, Biogeography and Community Ecology of Ants)
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8 pages, 256 KiB  
Review
Predators as Agents of Selection and Diversification
by Jerald B. Johnson and Mark C. Belk
Diversity 2020, 12(11), 415; https://doi.org/10.3390/d12110415 - 31 Oct 2020
Cited by 17 | Viewed by 10498
Abstract
Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can [...] Read more.
Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey upon common prey, in certain taxonomic groups where we still know very little, and in an overall effort to actually quantify mortality rates and the strength of natural selection in the wild. Full article
(This article belongs to the Special Issue Predators as Agents of Selection and Diversification)
16 pages, 2691 KiB  
Article
Site-Level Variation in Parrotfish Grazing and Bioerosion as a Function of Species-Specific Feeding Metrics
by Ines D Lange, Chris T Perry, Kyle M Morgan, Ronan Roche, Cassandra E Benkwitt and Nicholas AJ Graham
Diversity 2020, 12(10), 379; https://doi.org/10.3390/d12100379 - 2 Oct 2020
Cited by 24 | Viewed by 6258
Abstract
Parrotfish provide important ecological functions on coral reefs, including the provision of new settlement space through grazing and the generation of sediment through bioerosion of reef substrate. Estimating these functions at an ecosystem level depends on accurately quantifying the functional impact of individuals, [...] Read more.
Parrotfish provide important ecological functions on coral reefs, including the provision of new settlement space through grazing and the generation of sediment through bioerosion of reef substrate. Estimating these functions at an ecosystem level depends on accurately quantifying the functional impact of individuals, yet parrotfish feeding metrics are only available for a limited range of sites, species and size classes. We quantified bite rates, proportion of bites leaving scars and scar sizes in situ for the dominant excavator (Cetoscarus ocellatus, Chlorurus strongylocephalus, Ch. sordidus) and scraper species (Scarus rubroviolaceus, S. frenatus, S. niger, S. tricolor, S. scaber, S. psittacus) in the central Indian Ocean. This includes the first record of scar frequencies and sizes for the latter three species. Bite rates varied with species and life phase and decreased with body size. The proportion of bites leaving scars and scar sizes differed among species and increased with body size. Species-level allometric relationships between body size and each of these feeding metrics were used to parameterize annual individual grazing and bioerosion rates which increase non-linearly with body size. Large individuals of C. ocellatus, Ch. strongylocephalus and S. rubroviolaceus can graze 200–400 m2 and erode >500 kg of reef substrate annually. Smaller species graze 1–100 m2 yr−1 and erode 0.2–30 kg yr−1. We used these individual functional rates to quantify community grazing and bioerosion levels at 15 sites across the Maldives and the Chagos Archipelago. Although parrotfish density was 2.6 times higher on Maldivian reefs, average grazing (3.9 ± 1.4 m2 m−2 reef yr−1) and bioerosion levels (3.1 ± 1.2 kg m−2 reef yr−1) were about 15% lower than in the Chagos Archipelago (4.5 ± 2.3 and 3.7 ± 3.0, respectively), due to the dominance of small species and individuals in the Maldives (90% <30 cm length). This demonstrates that large-bodied species and individuals contribute disproportionally to both grazing and bioerosion. Across all sites, grazing increased by 66 ± 5 m2 ha−1 and bioerosion by 109 ± 9 kg ha−1 for every kg increase in parrotfish biomass. However, for a given level of parrotfish biomass, grazing and bioerosion levels were higher on Maldivian reefs than in the Chagos Archipelago. This suggests that small-bodied fish assemblages can maintain ecosystem functions, but only if key species are present in sufficiently high numbers. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Herbivorous Fish)
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16 pages, 557 KiB  
Article
Individual Variation in Predatory Behavior, Scavenging and Seasonal Prey Availability as Potential Drivers of Coexistence between Wolves and Bears
by Andrés Ordiz, Cyril Milleret, Antonio Uzal, Barbara Zimmermann, Petter Wabakken, Camilla Wikenros, Håkan Sand, Jon E Swenson and Jonas Kindberg
Diversity 2020, 12(9), 356; https://doi.org/10.3390/d12090356 - 15 Sep 2020
Cited by 29 | Viewed by 8993
Abstract
Several large carnivore populations are recovering former ranges, and it is important to understand interspecific interactions between overlapping species. In Scandinavia, recent research has reported that brown bear presence influences gray wolf habitat selection and kill rates. Here, we characterized the temporal use [...] Read more.
Several large carnivore populations are recovering former ranges, and it is important to understand interspecific interactions between overlapping species. In Scandinavia, recent research has reported that brown bear presence influences gray wolf habitat selection and kill rates. Here, we characterized the temporal use of a common prey resource by sympatric wolves and bears and described individual and seasonal variation in their direct and/or indirect interactions. Most bear–wolf interactions were indirect, via bear scavenging of wolf kills. Bears used >50% of wolf kills, whereas we did not record any wolf visit at bear kills. Adult and subadult bears visited wolf kills, but female bears with cubs of the year, the most vulnerable age class to conspecifics and other predators, did not. Wolf and bear kill rates peaked in early summer, when both targeted neonate moose calves, which coincided with a reduction in bear scavenging rate. Some bears were highly predatory and some did not kill any calf. Individual and age-class variation (in bear predation and scavenging patterns) and seasonality (in bear scavenging patterns and main prey availability of both wolves and bears) could mediate coexistence of these apex predators. Similar processes likely occur in other ecosystems with varying carnivore assemblages. Full article
(This article belongs to the Special Issue Ecology of Predation and Scavenging and the Interface)
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23 pages, 7291 KiB  
Article
Interspecific Hybridization and Introgression Influence Biodiversity—Based on Genetic Diversity of Central European Viola epipsila-V. palustris Complex
by Justyna Żabicka, Grzegorz Migdałek, Aneta Słomka, Elwira Sliwinska, Leszek Mackiewicz, Andrzej Keczyński and Elżbieta Kuta
Diversity 2020, 12(9), 321; https://doi.org/10.3390/d12090321 - 24 Aug 2020
Cited by 12 | Viewed by 4220
Abstract
The Viola epipsila-V. palustris complex is a highly taxonomically complicated group of species in its entire circumboreal range of distribution. Habitat loss, forest flooding, and hybridization could lead to the extinction of V. epipsila. A hybrid index and principal component [...] Read more.
The Viola epipsila-V. palustris complex is a highly taxonomically complicated group of species in its entire circumboreal range of distribution. Habitat loss, forest flooding, and hybridization could lead to the extinction of V. epipsila. A hybrid index and principal component analysis (PCA) were used to select qualitative and quantitative morphological features to distinguish parent species and hybrids, inter simple sequence repeat (ISSR) markers to determine the genetic diversity of the populations, flow cytometry to estimate the genome size (GS), and non-coding chloroplast DNA (cpDNA) regions to indicate the directions of crosses. All taxa are very morphologically variable, and their features can change within a season. The most stable feature is the distance of the bracts on the pedicel from the rhizome. The genetic diversity of all taxa populations is low and highly influenced by selfing and vegetative propagation. The population structure is differentiated: populations of V. epipsila or V. palustris, mixed populations with both parent species, F1 hybrids and populations with introgressive forms occur in different regions. The interspecific GS variation corresponds to the ploidy level (4x = 2.52 pg, 8x = 4.26 pg, 6x = 3.42 pg). Viola epipsila is the mother plant of the hybrids. Research has shown the risk of V. epipsila extinction in Central Europe and the importance of local populations in studying the role of hybridization in reducing/maintaining/increasing biodiversity. Full article
(This article belongs to the Special Issue Ecology, Biogeography and Evolutionary Biology of Peatlands)
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9 pages, 455 KiB  
Article
The Permeability of Natural versus Anthropogenic Forest Edges Modulates the Abundance of Ground Beetles of Different Dispersal Power and Habitat Affinity
by Tibor Magura and Gábor L. Lövei
Diversity 2020, 12(9), 320; https://doi.org/10.3390/d12090320 - 21 Aug 2020
Cited by 17 | Viewed by 3228
Abstract
Forest edges are formed by natural or anthropogenic processes and their maintaining processes cause fundamentally different edge responses. We evaluated the published evidence on the effect of various edges on the abundance of ground beetles of different habitat affinity and dispersal power. Our [...] Read more.
Forest edges are formed by natural or anthropogenic processes and their maintaining processes cause fundamentally different edge responses. We evaluated the published evidence on the effect of various edges on the abundance of ground beetles of different habitat affinity and dispersal power. Our results, based on 23 publications and 86 species, showed that natural forest edges were impenetrable for open-habitat species with high dispersal power, preventing their influx into the forest interiors, while forest specialist species of limited dispersal power penetrated and reached abundances comparable to those in forest interiors. Anthropogenic edges, maintained by continued disturbance were permeable by macropterous open-habitat species, allowing them to invade the forest interiors, while such edges (except the forestry-induced ones) deterred brachypterous forest specialists. Different permeability of forest edges with various maintaining processes can affect ecosystem functions and services, therefore the preservation and restoration of natural forest edges are key issues in both forest ecology and nature conservation. Full article
(This article belongs to the Special Issue Faunistical and Ecological Studies on Carabid Beetles)
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14 pages, 1325 KiB  
Article
The Differential Importance of Deep and Shallow Seagrass to Nekton Assemblages of the Great Barrier Reef
by Matthew A. Hayes, Eva C. McClure, Paul H. York, Kristin I. Jinks, Michael A. Rasheed, Marcus Sheaves and Rod M. Connolly
Diversity 2020, 12(8), 292; https://doi.org/10.3390/d12080292 - 27 Jul 2020
Cited by 14 | Viewed by 6446
Abstract
Seagrass meadows are an important habitat for a variety of animals, including ecologically and socioeconomically important species. Seagrass meadows are recognised as providing species with nursery grounds, and as a migratory pathway to adjacent habitats. Despite their recognised importance, little is known about [...] Read more.
Seagrass meadows are an important habitat for a variety of animals, including ecologically and socioeconomically important species. Seagrass meadows are recognised as providing species with nursery grounds, and as a migratory pathway to adjacent habitats. Despite their recognised importance, little is known about the species assemblages that occupy seagrass meadows of different depths in the coastal zone. Understanding differences in the distribution of species in seagrass at different depths, and differences in species diversity, abundance, biomass, and size spectra, is important to fully appreciate both the ecological significance and economic importance of these seagrass meadows. Here, we assess differences in the assemblage characteristics of fish, crustacea, and cephalopods (collectively, nekton) between deep (>9 m; Halophila spinulosa dominant) and shallow water (<2 m; Halodule uninervis and/or Zostera muelleri dominant) seagrass meadows of the central Great Barrier Reef coast of Queensland, Australia. Nekton assemblage structure differed between deep and shallow seagrass. Deeper meadows were typified by juvenile emperors (e.g., Lethrinus genivittatus), hairfinned leatherjacket (Paramonacanthus japonicus) and rabbitfish (e.g., Siganus fuscescens) in both biomass per unit effort (BPUE) and catch per unit effort (CPUE), whereas shallow meadows were typified by the green tiger prawn (Penaeus semisulcatus) and pugnose ponyfish (Secutor insidiator) in both BPUE and CPUE. Both meadow depths were distinct in their nekton assemblage, particularly for socioeconomically important species, with 11 species unique to both shallow and deep meadows. However, both meadow depths also included juveniles of socioeconomically important species found in adjacent habitats as adults. The total nekton CPUE was not different between deep and shallow seagrass, but the BPUE and body mass of individual animals were greater in deep than shallow seagrass. Size spectra analysis indicated that in both deep and shallow meadows, smaller animals predominated, even more so than theoretically expected for size spectra. Our findings highlight the unique attributes of both shallow and deeper water seagrass meadows, and identify the distinct and critically important role of deep seagrass meadows within the Great Barrier Reef World Heritage Area (GBRWHA) as a habitat for small and juvenile species, including those of local fisheries value. Full article
(This article belongs to the Special Issue Biodiversity in Seagrass Ecosystems)
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25 pages, 1905 KiB  
Article
Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis
by Marios Nikolaidis, Dimitris Mossialos, Stephen G. Oliver and Grigorios D. Amoutzias
Diversity 2020, 12(8), 289; https://doi.org/10.3390/d12080289 - 24 Jul 2020
Cited by 41 | Viewed by 9241
Abstract
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete [...] Read more.
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers. Full article
(This article belongs to the Special Issue Pseudomonas Biology and Biodiversity)
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23 pages, 1690 KiB  
Article
Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research
by Nuria Macías-Hernández, Marc Domènech, Pedro Cardoso, Brent C. Emerson, Paulo Alexandre Vieira Borges, Jesús Lozano-Fernandez, Octávio S. Paulo, Ana Vieira, Alba Enguídanos, François Rigal, Isabel R. Amorim and Miquel A. Arnedo
Diversity 2020, 12(8), 288; https://doi.org/10.3390/d12080288 - 23 Jul 2020
Cited by 22 | Viewed by 7353
Abstract
Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are [...] Read more.
Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies. Full article
(This article belongs to the Special Issue Systematics and Evolution of Spiders)
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22 pages, 4502 KiB  
Article
Plant Diversity Patterns and Conservation Implications under Climate-Change Scenarios in the Mediterranean: The Case of Crete (Aegean, Greece)
by Konstantinos Kougioumoutzis, Ioannis P. Kokkoris, Maria Panitsa, Panayiotis Trigas, Arne Strid and Panayotis Dimopoulos
Diversity 2020, 12(7), 270; https://doi.org/10.3390/d12070270 - 7 Jul 2020
Cited by 55 | Viewed by 10171
Abstract
Climate change poses a great challenge for biodiversity conservation. Several studies exist regarding climate change’s impacts on European plants, yet none has investigated how climate change will affect the extinction risk of the entire endemic flora of an island biodiversity hotspot, with intense [...] Read more.
Climate change poses a great challenge for biodiversity conservation. Several studies exist regarding climate change’s impacts on European plants, yet none has investigated how climate change will affect the extinction risk of the entire endemic flora of an island biodiversity hotspot, with intense human disturbance. Our aim is to assess climate change’s impacts on the biodiversity patterns of the endemic plants of Crete (S Aegean) and provide a case-study upon which a climate-smart conservation planning strategy might be set. We employed a variety of macroecological analyses and estimated the current and future biodiversity, conservation and extinction hotspots in Crete. We evaluated the effectiveness of climatic refugia and the Natura 2000 network of protected areas (PAs) for protecting the most vulnerable species and identified the taxa of conservation priority based on the Evolutionary Distinct and Globally Endangered (EDGE) index. The results revealed that high altitude areas of Cretan mountains constitute biodiversity hotspots and areas of high conservation and evolutionary value. Due to the “escalator to extinction” phenomenon, these areas are projected to become diversity “death-zones” and should thus be prioritised. Conservation efforts should be targeted at areas with overlaps among PAs and climatic refugia, characterised by high diversity and EDGE scores. This conservation-prioritisation planning will allow the preservation of evolutionary heritage, trait diversity and future ecosystem services for human well-being and acts as a pilot for similar regions worldwide. Full article
(This article belongs to the Special Issue Conservation and Management of Island Ecosystems)
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15 pages, 3474 KiB  
Article
Molecular Diversity of Nematode Parasites in Afrotropical Reed Frogs (Hyperolius spp.)
by Ulrich Sinsch, J. Maximilian Dehling, Patrick Scheid and Carsten Balczun
Diversity 2020, 12(7), 265; https://doi.org/10.3390/d12070265 - 2 Jul 2020
Cited by 12 | Viewed by 4196
Abstract
The diversity of nematodes infecting amphibians is understudied in tropical Africa and unknown in Rwanda. Diversity assessment is hampered by the fact that species descriptions refer mostly to morphological features that are unlinked to DNA sequences of marker genes available in public databases. [...] Read more.
The diversity of nematodes infecting amphibians is understudied in tropical Africa and unknown in Rwanda. Diversity assessment is hampered by the fact that species descriptions refer mostly to morphological features that are unlinked to DNA sequences of marker genes available in public databases. In this paper, we explore the abundance and diversity of parasitic nematodes in reed frogs Hyperolius kivuensis (n = 115), H. parallelus (n = 45) and H. viridiflavus (n = 100) collected in Rwanda. Five nematode species were identified morphologically as Orneoascaris chrysanthemoides, O. schoutedeni, Gendria leberrei, Aplectana chamaeleonis and Rhabdias collaris. Corresponding DNA sequences of 18S and COI genes were determined and subsequently deposited in GenBank. Aplectana chamaeleonis showed the highest prevalence (8.7%), but O. chrysanthemoides the highest mean intensity of infection (6.0) and largest number (24) of individuals in H. kivuensis. To the best of our knowledge, all amphibian hosts are new records for these nematode species, which are known to infect a wide range of amphibian and reptile species. Our findings suggest that nematode diversity is probably lower than previously assumed due to low host specificity. As morphological species identification is often challenging, our data facilitate molecular identification of adult and specifically larval nematodes found in amphibians of Sub-Saharan Africa. Full article
(This article belongs to the Section Animal Diversity)
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11 pages, 8586 KiB  
Article
Endosymbiotic Green Algae in Paramecium bursaria: A New Isolation Method and a Simple Diagnostic PCR Approach for the Identification
by Christian Spanner, Tatyana Darienko, Tracy Biehler, Bettina Sonntag and Thomas Pröschold
Diversity 2020, 12(6), 240; https://doi.org/10.3390/d12060240 - 12 Jun 2020
Cited by 15 | Viewed by 6683
Abstract
Paramecium bursaria is a single-celled model organism for studying endosymbiosis among ciliates and green algae. Most strains of P. bursaria bear either Chlorella variabilis or Micractinium conductrix as endosymbionts. Both algal genera are unicellular green algae characterized by cup-shaped chloroplasts containing a single [...] Read more.
Paramecium bursaria is a single-celled model organism for studying endosymbiosis among ciliates and green algae. Most strains of P. bursaria bear either Chlorella variabilis or Micractinium conductrix as endosymbionts. Both algal genera are unicellular green algae characterized by cup-shaped chloroplasts containing a single pyrenoid and reproduction by autospores. Due to their size and only few morphological characteristics, these green algae are very difficult to discriminate by microscopy only. Their cultivation is laborious and often unsuccessful, but we developed a three-step isolation method, which provided axenic cultures of endosymbionts. In addition to the time-consuming isolation, we developed a simple diagnostic PCR identification method using specific primers for C. variabilis and M. conductrix that provided reliable results. One advantage of this approach was that the algae do not have to be isolated from their host. For a comparative study, we investigated 19 strains of P. bursaria from all over the world (new isolates and available laboratory strains) belonging to the five known syngens (R1–R5). Six European ciliate strains belonging to syngens R1 and R2 bore M. conductrix as endosymbiont whereas C. variabilis was discovered in syngens R1–R5 having worldwide origins. Our results reveal the first evidence of C. variabilis as endosymbiont in P. bursaria in Europe. Full article
(This article belongs to the Special Issue Biodiversity of Ciliates and their Symbionts)
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11 pages, 2168 KiB  
Article
Genetic Approaches Are Necessary to Accurately Understand Bat-Wind Turbine Impacts
by Austin S. Chipps, Amanda M. Hale, Sara P. Weaver and Dean A. Williams
Diversity 2020, 12(6), 236; https://doi.org/10.3390/d12060236 - 11 Jun 2020
Cited by 16 | Viewed by 4658
Abstract
Bats are killed at wind energy facilities worldwide and we must improve our understanding of why this is happening and implement effective strategies to minimize impacts. To this end, we need accurate assessments of which individuals from which bat species are being killed [...] Read more.
Bats are killed at wind energy facilities worldwide and we must improve our understanding of why this is happening and implement effective strategies to minimize impacts. To this end, we need accurate assessments of which individuals from which bat species are being killed at individual wind projects and at regional and range-wide scales. Traditional fatality searches have relied on physical characteristics to ascertain species and sex of bat carcasses collected at wind turbines; however, the resulting data can be incomplete and inaccurate. In contrast, the use of readily available and low-cost molecular methods improves both the quality and quantity of available data. We applied such methods to a bat fatality dataset (n = 439 bats) from far-south Texas, USA. Using DNA barcoding, we increased accurate species identification from 83% to 97%, and discovered the presence of 2 bat species outside of their known geographic ranges. Using a PCR-based approach to determine sex, the number of carcasses with correct sex assignment increased from 35% to 94%, and we documented a female-biased sex ratio for all species combined and for Dasypterus ega. We recommend that molecular methods be used during future survey efforts to accurately assess the impacts of wind energy on bats. Full article
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18 pages, 2209 KiB  
Article
Diversification of African Rainforest Restricted Clades: Piptostigmateae and Annickieae (Annonaceae)
by Baptiste Brée, Andrew J. Helmstetter, Kévin Bethune, Jean-Paul Ghogue, Bonaventure Sonké and Thomas L. P. Couvreur
Diversity 2020, 12(6), 227; https://doi.org/10.3390/d12060227 - 7 Jun 2020
Cited by 13 | Viewed by 4429
Abstract
African rainforests (ARFs) are species rich and occur in two main rainforest blocks: West/Central and East Africa. This diversity is suggested to be the result of recent diversification, high extinction rates and multiple vicariance events between west/central and East African forests. We reconstructed [...] Read more.
African rainforests (ARFs) are species rich and occur in two main rainforest blocks: West/Central and East Africa. This diversity is suggested to be the result of recent diversification, high extinction rates and multiple vicariance events between west/central and East African forests. We reconstructed the diversification history of two subtribes (Annickieae and Piptostigmateae) from the ecologically dominant and diverse tropical rainforest plant family Annonaceae. Both tribes contain endemic taxa in the rainforests of West/Central and East Africa. Using a dated molecular phylogeny based on 32 nuclear markers, we estimated the timing of the origin of East African species. We then undertook several diversification analyses focusing on Piptostigmateae to infer variation in speciation and extinction rates, and test the impact of extinction events. Speciation in both tribes dated to the Pliocene and Pleistocene. In particular, Piptostigma (13 species) diversified mainly during the Pleistocene, representing one of the few examples of Pleistocene speciation in an African tree genus. Our results also provide evidence of an ARF fragmentation at the mid-Miocene linked to climatic changes across the region. Overall, our results suggest that continental-wide forest fragmentation during the Neogene (23.03–2.58 Myr), and potentially during the Pliocene, led to one or possibly two vicariance events within the ARF clade Piptostigmateae, in line with other studies. Among those tested, the best fitting diversification model was the one with an exponential speciation rate and no extinction. We did not detect any evidence of mass extinction events. This study gives weight to the idea that the ARF might not have been so negatively impacted by extinction during the Neogene, and that speciation mainly took place during the Pliocene and Pleistocene. Full article
(This article belongs to the Special Issue Biodiversity of Vegetation and Flora in Tropical Africa)
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16 pages, 974 KiB  
Article
Rusty Blackbird Habitat Selection and Survivorship during Nesting and Post-Fledging
by Patricia J. Wohner, Carol R. Foss and Robert J. Cooper
Diversity 2020, 12(6), 221; https://doi.org/10.3390/d12060221 - 2 Jun 2020
Cited by 5 | Viewed by 3563
Abstract
Rusty blackbird (Euphagus carolinus) populations have declined dramatically since the 1970s and the cause of decline is still unclear. As is the case for many passerines, most research on rusty blackbirds occurs during the nesting period. Nest success is relatively high [...] Read more.
Rusty blackbird (Euphagus carolinus) populations have declined dramatically since the 1970s and the cause of decline is still unclear. As is the case for many passerines, most research on rusty blackbirds occurs during the nesting period. Nest success is relatively high in most of the rusty blackbird’s range, but survival during the post-fledging period, when fledgling songbirds are particularly vulnerable, has not been studied. We assessed fledgling and adult survivorship and nest success in northern New Hampshire from May to August in 2010 to 2012. We also assessed fledgling and adult post-fledging habitat selection and nest-site selection. The likelihood of rusty blackbirds nesting in a given area increased with an increasing proportion of softwood/mixed-wood sapling stands and decreasing distances to first to sixth order streams. Wetlands were not selected for nest sites, but both adults and fledglings selected wetlands for post-fledging habitat. Fledglings and adults selected similar habitat post-fledging, but fledglings were much more likely to be found in habitat with an increasing proportion of softwood/mixed-wood sapling stands and were more likely to be closer to streams than adults. No habitat variables selected during nesting or post-fledging influenced daily survival rates, which were relatively low for adults over the 60-day study periods (males 0.996, females 0.998). Fledgling survival rates (0.89) were much higher than reported for species of similar size. Full article
(This article belongs to the Special Issue Boreal Bird Ecology, Management and Conservation)
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16 pages, 3236 KiB  
Review
River Capture and Freshwater Biological Evolution: A Review of Galaxiid Fish Vicariance
by Jonathan M. Waters, Christopher P. Burridge and Dave Craw
Diversity 2020, 12(6), 216; https://doi.org/10.3390/d12060216 - 29 May 2020
Cited by 36 | Viewed by 5230
Abstract
Geological processes can strongly affect the distribution and diversification of freshwater-limited species. In particular, a combination of geological and biological data has suggested that Earth history processes can drive vicariant isolation and speciation in non-migratory freshwater fishes. Here, we synthesise recently published geological [...] Read more.
Geological processes can strongly affect the distribution and diversification of freshwater-limited species. In particular, a combination of geological and biological data has suggested that Earth history processes can drive vicariant isolation and speciation in non-migratory freshwater fishes. Here, we synthesise recently published geological and freshwater phylogeographic data to illustrate that changes in river drainage geometry are important drivers of galaxiid diversification, both in New Zealand and elsewhere. Major river capture events have led to the isolation and divergence of unique and geographically-restricted lineages, including taxa that are now of prime conservation concern. The parallel phylogeographic effects of drainage shifts have been verified by observations of concordant patterns in co-distributed species. Broadly, this study highlights the dynamic interplay between physical and biological processes in geologically active settings. Full article
(This article belongs to the Special Issue Evolutionary Genetics and Biogeography of Galaxiid Fishes)
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19 pages, 1705 KiB  
Article
Highlighting the Crude Oil Bioremediation Potential of Marine Fungi Isolated from the Port of Oran (Algeria)
by Ahlem Maamar, Marie-Elisabeth Lucchesi, Stella Debaets, Nicolas Nguyen van Long, Maxence Quemener, Emmanuel Coton, Mohammed Bouderbala, Gaëtan Burgaud and Amaria Matallah-Boutiba
Diversity 2020, 12(5), 196; https://doi.org/10.3390/d12050196 - 15 May 2020
Cited by 46 | Viewed by 9633
Abstract
While over hundreds of terrestrial fungal genera have been shown to play important roles in the biodegradation of hydrocarbons, few studies have so far focused on the fungal bioremediation potential of petroleum in the marine environment. In this study, the culturable fungal communities [...] Read more.
While over hundreds of terrestrial fungal genera have been shown to play important roles in the biodegradation of hydrocarbons, few studies have so far focused on the fungal bioremediation potential of petroleum in the marine environment. In this study, the culturable fungal communities occurring in the port of Oran in Algeria, considered here as a chronically-contaminated site, have been mainly analyzed in terms of species richness. A collection of 84 filamentous fungi has been established from seawater samples and then the fungi were screened for their ability to utilize and degrade crude oil. A total of 12 isolates were able to utilize crude oil as a unique carbon source, from which 4 were defined as the most promising biodegrading isolates based on a screening test using 2,6-dichlorophenol indophenol as a proxy to highlight their ability to metabolize crude oil. The biosurfactant production capability was also tested and, interestingly, the oil spreading and drop-collapse tests highlighted that the 4 most promising isolates were also those able to produce the highest quantity of biosurfactants. The results generated in this study demonstrate that the most promising fungal isolates, namely Penicillium polonicum AMF16, P. chrysogenum AMF47 and 2 isolates (AMF40 and AMF74) affiliated to P. cyclopium, appear to be interesting candidates for bioremediation of crude oil pollution in the marine environment within the frame of bioaugmentation or biostimulation processes. Full article
(This article belongs to the Section Microbial Diversity and Culture Collections)
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15 pages, 7899 KiB  
Article
Micractinium tetrahymenae (Trebouxiophyceae, Chlorophyta), a New Endosymbiont Isolated from Ciliates
by Thomas Pröschold, Gianna Pitsch and Tatyana Darienko
Diversity 2020, 12(5), 200; https://doi.org/10.3390/d12050200 - 15 May 2020
Cited by 15 | Viewed by 6298
Abstract
Endosymbiosis between coccoid green algae and ciliates are widely distributed and occur in various phylogenetic lineages among the Ciliophora. Most mixotrophic ciliates live in symbiosis with different species and genera of the so-called Chlorella clade (Trebouxiophyceae). The mixotrophic ciliates can be differentiated into [...] Read more.
Endosymbiosis between coccoid green algae and ciliates are widely distributed and occur in various phylogenetic lineages among the Ciliophora. Most mixotrophic ciliates live in symbiosis with different species and genera of the so-called Chlorella clade (Trebouxiophyceae). The mixotrophic ciliates can be differentiated into two groups: (i) obligate, which always live in symbiosis with such green algae and are rarely algae-free and (ii) facultative, which formed under certain circumstances such as in anoxic environments an association with algae. A case of the facultative endosymbiosis is found in the recently described species of Tetrahymena, T. utriculariae, which lives in the bladder traps of the carnivorous aquatic plant Utricularia reflexa. The green endosymbiont of this ciliate belonged to the genus Micractinium. We characterized the isolated algal strain using an integrative approach and compared it to all described species of this genus. The phylogenetic analyses using complex evolutionary secondary structure-based models revealed that this endosymbiont represents a new species of Micractinium, M. tetrahymenae sp. nov., which was further confirmed by the ITS2/CBC approach. Full article
(This article belongs to the Special Issue Biodiversity of Ciliates and their Symbionts)
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12 pages, 1934 KiB  
Article
Longitude, Forest Fragmentation, and Plant Size Influence Cycas micronesica Mortality Following Island Insect Invasions
by Thomas E. Marler and Murukesan V. Krishnapillai
Diversity 2020, 12(5), 194; https://doi.org/10.3390/d12050194 - 14 May 2020
Cited by 20 | Viewed by 5872
Abstract
Island invasions may cause severe changes in biodiversity, but the factors that influence these changes are not well understood. We established 120 plots in Cycas micronesica habitats throughout Guam in 2005 following the invasion of the armored scale Aulacaspis yasumatsui, then observed [...] Read more.
Island invasions may cause severe changes in biodiversity, but the factors that influence these changes are not well understood. We established 120 plots in Cycas micronesica habitats throughout Guam in 2005 following the invasion of the armored scale Aulacaspis yasumatsui, then observed plant mortality through 2020. We used transects in Yap as benchmarks, as the Yap C. micronesica population is not threatened. The initial Guam plots contained about 1600 seedlings, 1160 juveniles, and 1240 mature plants per ha. Seedling mortality was 100% by 2006, juvenile mortality was 100% by 2014, and the 2020 census revealed 96% mortality of the plant population. Localities in western Guam and isolated forest fragments exhibited the greatest mortality, with 100% extirpation from two fragmented western localities. The juvenile and mature trees in Yap were unchanged from 2010 to 2018, but the seedling count was heterogeneous among the years. Constrained recruitment from seedlings to juveniles explained these dynamics. Yap transects contained about 6120 seedlings, 3400 juveniles, and 1250 mature plants per ha. Biological control of the invasive insects remains the acute conservation action needed for the Guam population. Lessons learned may be useful in other regions where invasions of non-native pests threaten biodiversity. Full article
(This article belongs to the Section Biodiversity Conservation)
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9 pages, 1304 KiB  
Communication
High Prevalence of Novel Beak and Feather Disease Virus in Sympatric Invasive Parakeets Introduced to Spain From Asia and South America
by Francisco Morinha, Martina Carrete, José L. Tella and Guillermo Blanco
Diversity 2020, 12(5), 192; https://doi.org/10.3390/d12050192 - 13 May 2020
Cited by 26 | Viewed by 6856
Abstract
The psittacine beak and feather disease (PBFD) is a globally widespread infectious bird disease that mainly affects species within the Order Psittaciformes (parrots and allies). The disease is caused by an avian circovirus (the beak and feather disease virus, BFDV), which is highly [...] Read more.
The psittacine beak and feather disease (PBFD) is a globally widespread infectious bird disease that mainly affects species within the Order Psittaciformes (parrots and allies). The disease is caused by an avian circovirus (the beak and feather disease virus, BFDV), which is highly infectious and can lead to severe consequences in wild and captive populations during an outbreak. Both legal and illegal trading have spread the BFDV around the world, although little is known about its prevalence in invasive parrot populations. Here, we analyze the BFDV prevalence in sympatric invasive populations of rose-ringed (Psittacula krameri) and monk parakeets (Myiopsitta monachus) in Southern Spain. We PCR-screened 110 blood samples (55 individuals from each species) for BFDV and characterized the genotypes of five positives from each species. About 33% of rose-ringed parakeets and 37% of monk parakeets sampled were positive for BFDV, while neither species showed disease symptoms. The circovirus identified is a novel BFDV genotype common to both species, similar to the BFDV genotypes detected in several parrot species kept in captivity in Saudi Arabia, South Africa and China. Our data evidences the importance of an accurate evaluation of avian diseases in wild populations, since invasive parrots may be bringing BFDV without showing any visually detectable clinical sign. Further research on the BFDV prevalence and transmission (individual–individual, captive–wild and wild–captive) in different bird orders and countries is crucial to understand the dynamics of the viral infection and minimize its impact in captive and wild populations. Full article
(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)
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20 pages, 2745 KiB  
Article
Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient
by Silvia Bianchelli, Daniele Nizzoli, Marco Bartoli, Pierluigi Viaroli, Eugenio Rastelli and Antonio Pusceddu
Diversity 2020, 12(5), 189; https://doi.org/10.3390/d12050189 - 12 May 2020
Cited by 11 | Viewed by 4532
Abstract
In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities [...] Read more.
In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities are influenced by multiple environmental variables, which can vary across different habitats. However, analyses of these relationships have mostly been conducted by considering the different habitats separately, even though freshwater, transitional, and marine ecosystems, physically linked to each other, are not worlds apart. Here, we investigated the quantity and nutritional quality of sedimentary OM, along with the prokaryotic and meiofauna abundance, biomass, and biodiversity, in two sampling periods, corresponding to high vs. low freshwater inputs to the sea, along a river-to-sea transect. The highest values of sedimentary organic loads and their nutritional quality, prokaryotic and meiofaunal abundance, and biomass were consistently observed in lagoon systems. Differences in the prokaryotic Operational Taxonomic Units (OTUs) and meiofaunal taxonomic composition, rather than changes in the richness of taxa, were observed among the three habitats and, in each habitat, between sampling periods. Such differences were driven by either physical or trophic variables, though with differences between seasons. Overall, our results indicate that the apparent positive relationship between sedimentary OM, prokaryote and meiofaunal abundance, and biomass across the river-lagoon-sea transect under scrutiny is more the result of a pattern of specifically adapted prokaryotic and meiofaunal communities to different habitats, rather than an actually positive ‘response’ to OM enrichment. We conclude that the synoptic analysis of prokaryotes and meiofauna can provide useful information on the relative effect of organic enrichment and environmental settings across gradients of environmental continuums, including rivers, lagoons, and marine coastal ecosystems. Full article
(This article belongs to the Special Issue Meiofauna Biodiversity and Ecology)
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21 pages, 2806 KiB  
Article
Morphological Convergence and Divergence in Galaxias Fishes in Lentic and Lotic Habitats
by Nicholas R. Dunn, Leanne K. O’Brien, Christopher P. Burridge and Gerard P. Closs
Diversity 2020, 12(5), 183; https://doi.org/10.3390/d12050183 - 8 May 2020
Cited by 16 | Viewed by 4973
Abstract
The influence of contrasting lentic and lotic hydrological environments on the morphology of members of the Galaxias vulgaris species complex was examined. Morphological variation between habitat types was investigated by comparison of populations of Galaxias brevipinnis (inferred ancestor), Galaxias gollumoides (roundhead morphotype) and [...] Read more.
The influence of contrasting lentic and lotic hydrological environments on the morphology of members of the Galaxias vulgaris species complex was examined. Morphological variation between habitat types was investigated by comparison of populations of Galaxias brevipinnis (inferred ancestor), Galaxias gollumoides (roundhead morphotype) and Galaxias vulgaris (flathead morphotype). Interspecific convergence and intraspecific divergence of morphological characters were demonstrated, representing general shifts in morphology towards a common functional form in particular hydrological environments. In all species, more lentic Galaxias had longer bodies; shorter, more stout caudal peduncles; longer, narrower pectoral fins; and longer, wider heads with larger mouths. In comparison, lotic Galaxias had relatively shorter bodies; more slender caudal peduncles; broader pectoral fins; and shorter flatter heads, with smaller mouths. This study suggests that the hydrological environment of a habitat is an important factor moulding and maintaining an individual fish’s morphology to a particular habitat type, most likely representing a phenotypic plastic response. Full article
(This article belongs to the Special Issue Evolutionary Genetics and Biogeography of Galaxiid Fishes)
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15 pages, 2372 KiB  
Article
Species Diversity of Micromycetes Associated with Epipactis helleborine and Epipactis purpurata (Orchidaceae, Neottieae) in Southwestern Poland
by Rafał Ogórek, Klaudia Kurczaba, Zbigniew Łobas, Elżbieta Żołubak and Anna Jakubska-Busse
Diversity 2020, 12(5), 182; https://doi.org/10.3390/d12050182 - 7 May 2020
Cited by 12 | Viewed by 5423
Abstract
The Orchidaceae family is a diverse family of flowering plants that occur naturally in most parts of the world. However, fungal communities inhabiting different parts of orchids are not sufficiently described. The aim of the study was to conduct a mycological evaluation of [...] Read more.
The Orchidaceae family is a diverse family of flowering plants that occur naturally in most parts of the world. However, fungal communities inhabiting different parts of orchids are not sufficiently described. The aim of the study was to conduct a mycological evaluation of Epipactis helleborine and E. purpurata (Orchidaceae), which grow naturally in Lower Silesia (SW Poland), by identifying the species composition of the culturable micromycetes fungi on the surfaces of the plants and from the inner layers of the tissues. Fungi were identified based on a phenotypic and genotypic analysis. To our knowledge, this is the first such analysis. This study showed that more species of micromycetes were cultured from E. helleborine compared with E. purpurata. The flowering plants of E. helleborine were inhabited by the largest number of culturable fungal species (13 species), and the fewest species were isolated from the flowering plants of E. purpurata (eight species). Some of these fungal species may be pathogens of the plants. The surface tissues of the orchids were mainly inhabited by Mucor moelleri and/or Penicillium biourgeianum. The inner layers of these plants were the most colonized by Alternaria tenuissima and/or Arthrinium arundinis and/or Fusarium sporotrichioides. The relative dominance of these fungal species depended mainly on the development phase of the plants. Full article
(This article belongs to the Special Issue The Ecology and Diversity of Orchids)
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10 pages, 658 KiB  
Review
Potential of DNA Intercalating Alkaloids and Other Plant Secondary Metabolites against SARS-CoV-2 Causing COVID-19
by Michael Wink
Diversity 2020, 12(5), 175; https://doi.org/10.3390/d12050175 - 30 Apr 2020
Cited by 110 | Viewed by 13647
Abstract
Many plants produce secondary metabolites (PSMs) with antiviral activities. Among the antiviral PSMs, lipophilic terpenoids in essential oils can disturb the lipid envelope of viruses. Phenols and polyphenols (flavonoids, rosmarinic acid and tannins) attack viral proteins present in the viral membrane or inside [...] Read more.
Many plants produce secondary metabolites (PSMs) with antiviral activities. Among the antiviral PSMs, lipophilic terpenoids in essential oils can disturb the lipid envelope of viruses. Phenols and polyphenols (flavonoids, rosmarinic acid and tannins) attack viral proteins present in the viral membrane or inside the virus particle. Both phenolics and essential oils are active against free viral particles but not—or to a lesser degree—after a virus has entered a host cell. Another group of PSMs is directed against DNA or RNA. These are DNA intercalators such as sanguinarine, berberine, emetine and other isoquinoline alkaloids, ß-carboline, and quinoline alkaloids such as quinine, cinchonine, dictamine and skimmianine. The DNA intercalators stabilize double-stranded nucleic acids and inhibit the replication, transcription, and translation of genetic material. These alkaloids can inhibit viral development and viral replication in cells, as shown for SARS-CoV-1 and other viruses. Since chloroquine (which is also a DNA intercalator and a chemical derivative of the alkaloid quinine) is apparently clinically helpful against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, it is assumed that intercalating alkaloids, or the medicinal plants producing them, may be interesting candidates for the development of new antiviral drugs for the treatment of coronavirus disease 2019 (COVID-19). Full article
(This article belongs to the Section Chemical Diversity and Chemical Ecology)
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14 pages, 1322 KiB  
Article
Switching LPS to LED Streetlight May Dramatically Reduce Activity and Foraging of Bats
by Christian Kerbiriou, Kévin Barré, Léa Mariton, Julie Pauwels, Georges Zissis, Alexandre Robert and Isabelle Le Viol
Diversity 2020, 12(4), 165; https://doi.org/10.3390/d12040165 - 24 Apr 2020
Cited by 21 | Viewed by 8591
Abstract
Artificial light at night is considered a major threat to biodiversity, especially for nocturnal species, as it reduces habitat availability, quality, and functionality. Since the recent evolution in light technologies in improving luminous efficacy, developed countries are experiencing a renewal of their lighting [...] Read more.
Artificial light at night is considered a major threat to biodiversity, especially for nocturnal species, as it reduces habitat availability, quality, and functionality. Since the recent evolution in light technologies in improving luminous efficacy, developed countries are experiencing a renewal of their lighting equipment that reaches its end-of-life, from conventional lighting technologies to light emitting diodes (LEDs). Despite potential cascading impacts of such a shift on nocturnal fauna, few studies have so far dealt with the impact of the renewal of street lighting by new technologies. Specifically, only one study, by Rowse et al.2016, examined the effects of switching from widely used low pressure sodium (LPS) lamps to LEDs, using bats as biological models. This study was based on a before-after-control-impact paired design (BACIP) at 12 pairs in the UK, each including one control and one experimental streetlight. If Rowse et al. 2016 showed no effect of switching to LEDs streetlights on bat activity, the effects of respective changes in light intensity and spectrum were not disentangled when testing switch effects. Here, we conduct a retrospective analysis of their data to include these covariates in statistical models with the aim of disentangling the relative effects of these light characteristics. Our re-analysis clearly indicates that the switches in spectrum and in intensity with replacement of LPS with LED lamps have significant additive and interactive effects, on bat activity. We also show that bat activity and buzz ratio decrease with increasing LED intensity while an opposite effect is observed with LPS lamps. Hence, the loss or the gain in bat activity when lamp types, i.e., spectrum, are switched strongly depends on the initial and new lamp intensities. Our results stress the need to consider simultaneously the effects of changes in the different lights characteristics when street lighting changes. Because switches from LPS to LED lamps can lead to an increase in light intensity, such technological changes may involve a reduction of bat activity in numerous cases, especially at high LED intensities. Since we are currently at an important crossroad in lighting management, we recommend to limit LED intensity and improve its spectral composition toward warmer colors to limit potential deleterious impacts on bat activity. Full article
(This article belongs to the Special Issue Impacts of Pressure on Bat Populations)
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28 pages, 2278 KiB  
Article
Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation
by Peter Houde, Edward L. Braun and Lawrence Zhou
Diversity 2020, 12(4), 164; https://doi.org/10.3390/d12040164 - 23 Apr 2020
Cited by 12 | Viewed by 5129
Abstract
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene ( [...] Read more.
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction. Full article
(This article belongs to the Special Issue Origins of Modern Avian Biodiversity)
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12 pages, 249 KiB  
Article
A Common Approach to the Conservation of Threatened Island Vascular Plants: First Results in the Mediterranean Basin
by Giuseppe Fenu, Gianluigi Bacchetta, Charalambos S. Christodoulou, Donatella Cogoni, Christini Fournaraki, Giusso del Galdo Gian Pietro, Panagiota Gotsiou, Angelos Kyratzis, Carole Piazza, Magdalena Vicens and Bertrand de Montmollin
Diversity 2020, 12(4), 157; https://doi.org/10.3390/d12040157 - 18 Apr 2020
Cited by 49 | Viewed by 7374
Abstract
The Mediterranean islands represent a center of vascular plant diversity featuring a high rate of endemic richness. Such richness is highly threatened, however, with many plants facing the risk of extinction and in need of urgent protection measures. The CARE-MEDIFLORA project promoted the [...] Read more.
The Mediterranean islands represent a center of vascular plant diversity featuring a high rate of endemic richness. Such richness is highly threatened, however, with many plants facing the risk of extinction and in need of urgent protection measures. The CARE-MEDIFLORA project promoted the use of ex situ collections to experiment with in situ active actions for threatened plants. Based on common criteria, a priority list of target plant species was elaborated, and germplasm conservation, curation and storage in seed banks was carried out. Accessions were duplicated in the seed banks of the partners or other institutions. Germination experiments were carried out on a selected group of threatened species. A total of 740 accessions from 429 vascular plants were stored in seed banks, and 410 seed germination experiments for 283 plants species were completed; a total of 63 in situ conservation actions were implemented, adopting different methodological protocols. For each conservation program, a specific monitoring protocol was implemented in collaboration with local and regional authorities. This project represents the first attempt to develop common strategies and an opportunity to join methods and methodologies focused on the conservation of threatened plants in unique natural laboratories such as the Mediterranean islands. Full article
(This article belongs to the Special Issue In Situ and Ex Situ Biodiversity Conservation)
22 pages, 5548 KiB  
Article
Coral Restoration Effectiveness: Multiregional Snapshots of the Long-Term Responses of Coral Assemblages to Restoration
by Margaux Y. Hein, Roger Beeden, Alastair Birtles, Naomi M. Gardiner, Thomas Le Berre, Jessica Levy, Nadine Marshall, Chad M. Scott, Lisa Terry and Bette L. Willis
Diversity 2020, 12(4), 153; https://doi.org/10.3390/d12040153 - 17 Apr 2020
Cited by 57 | Viewed by 11175
Abstract
Coral restoration is rapidly becoming a mainstream strategic reef management response to address dramatic declines in coral cover worldwide. Restoration success can be defined as enhanced reef functions leading to improved ecosystem services, with multiple benefits at socio-ecological scales. However, there is often [...] Read more.
Coral restoration is rapidly becoming a mainstream strategic reef management response to address dramatic declines in coral cover worldwide. Restoration success can be defined as enhanced reef functions leading to improved ecosystem services, with multiple benefits at socio-ecological scales. However, there is often a mismatch between the objectives of coral restoration programs and the metrics used to assess their effectiveness. In particular, the scales of ecological benefits currently assessed are typically limited in both time and space, often being limited to short-term monitoring of the growth and survival of transplanted corals. In this paper, we explore reef-scale responses of coral assemblages to restoration practices applied in four well-established coral restoration programs. We found that hard coral cover and structural complexity were consistently greater at restored compared to unrestored (degraded) sites. However, patterns in coral diversity, coral recruitment, and coral health among restored, unrestored, and reference sites varied across locations, highlighting differences in methodologies among restoration programs. Altogether, differences in program objectives, methodologies, and the state of nearby coral communities were key drivers of variability in the responses of coral assemblages to restoration. The framework presented here provides guidance to improve qualitative and quantitative assessments of coral restoration efforts and can be applied to further understanding of the role of restoration within resilience-based reef management. Full article
(This article belongs to the Section Biodiversity Conservation)
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8 pages, 1534 KiB  
Communication
Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients
by Harmen P. Doekes, Ino Curik, István Nagy, János Farkas, György Kövér and Jack J. Windig
Diversity 2020, 12(4), 155; https://doi.org/10.3390/d12040155 - 17 Apr 2020
Cited by 31 | Viewed by 9111
Abstract
To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski’s ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be [...] Read more.
To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski’s ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of FANC and FNEW, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The FANC was systematically underestimated and consequently, FNEW was overestimated. To illustrate this bias, we calculated FANC and FNEW by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of FANC and FNEW, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of FANC and FNEW. Full article
(This article belongs to the Section Biodiversity Conservation)
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22 pages, 3684 KiB  
Article
Identifying Mechanisms for Successful Ecological Restoration with Salvaged Topsoil in Coastal Sage Scrub Communities
by Katharina T. Schmidt, Mia Maltz, Priscilla Ta, Banafshe Khalili, Claudia Weihe, Michala Phillips, Emma Aronson, Megan Lulow, Jennifer Long and Sarah Kimball
Diversity 2020, 12(4), 150; https://doi.org/10.3390/d12040150 - 14 Apr 2020
Cited by 17 | Viewed by 7116
Abstract
Although aboveground metrics remain the standard, restoring functional ecosystems should promote both aboveground and belowground biotic communities. Restoration using salvaged soil—removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites—is an alternative to traditional methods. Salvaged soil [...] Read more.
Although aboveground metrics remain the standard, restoring functional ecosystems should promote both aboveground and belowground biotic communities. Restoration using salvaged soil—removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites—is an alternative to traditional methods. Salvaged soil contains both seed and spore banks, which may holistically augment restoration. Salvaged soil methods may reduce non-native germination by burying non-native seeds, increase native diversity by adding native seeds, or transfer soil microbiomes, including arbuscular mycorrhizal fungi (AMF), to recipient sites. We transferred soil to three degraded recipient sites and monitored soil microbes, using flow cytometry and molecular analyses, and characterized the plant community composition. Our findings suggest that salvaged soil at depths ≥5 cm reduced non-native grass cover and increased native plant density and species richness. Bacterial abundance at recipient sites were statistically equivalent to donor sites in abundance. Overall, topsoil additions affected AMF alpha diversity and community composition and increased rhizophilic AMF richness. Because salvaged soil restoration combines multiple soil components, including native plant and microbial propagules, it may promote both aboveground and belowground qualities of the donor site, when applying this method for restoring invaded and degraded ecosystems. Full article
(This article belongs to the Special Issue Microbial Interactions with Invasive Plant Species)
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39 pages, 884 KiB  
Review
Knowing the Enemy: Inducible Defences in Freshwater Zooplankton
by Patricia Diel, Marvin Kiene, Dominik Martin-Creuzburg and Christian Laforsch
Diversity 2020, 12(4), 147; https://doi.org/10.3390/d12040147 - 7 Apr 2020
Cited by 46 | Viewed by 8941
Abstract
Phenotypic plasticity in defensive traits is an appropriate mechanism to cope with the variable hazard of a frequently changing predator spectrum. In the animal kingdom these so-called inducible defences cover the entire taxonomic range from protozoans to vertebrates. The inducible defensive traits range [...] Read more.
Phenotypic plasticity in defensive traits is an appropriate mechanism to cope with the variable hazard of a frequently changing predator spectrum. In the animal kingdom these so-called inducible defences cover the entire taxonomic range from protozoans to vertebrates. The inducible defensive traits range from behaviour, morphology, and life-history adaptations to the activation of specific immune systems in vertebrates. Inducible defences in prey species play important roles in the dynamics and functioning of food webs. Freshwater zooplankton show the most prominent examples of inducible defences triggered by chemical cues, so-called kairomones, released by predatory invertebrates and fish. The objective of this review is to highlight recent progress in research on inducible defences in freshwater zooplankton concerning behaviour, morphology, and life-history, as well as difficulties of studies conducted in a multipredator set up. Furthermore, we outline costs associated with the defences and discuss difficulties as well as the progress made in characterizing defence-inducing cues. Finally, we aim to indicate further possible routes in this field of research and provide a comprehensive table of inducible defences with respect to both prey and predator species. Full article
(This article belongs to the Special Issue Predators as Agents of Selection and Diversification)
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18 pages, 4576 KiB  
Article
News from the Sea: A New Genus and Seven New Species in the Pleosporalean Families Roussoellaceae and Thyridariaceae
by Anna Poli, Elena Bovio, Lucrezia Ranieri, Giovanna Cristina Varese and Valeria Prigione
Diversity 2020, 12(4), 144; https://doi.org/10.3390/d12040144 - 6 Apr 2020
Cited by 38 | Viewed by 5243
Abstract
Nineteen fungal strains associated with the seagrass Posidonia oceanica, with the green alga Flabellia petiolata, and the brown alga Padina pavonica were collected in the Mediterranean Sea. These strains were previously identified at the family level and hypothesised to be undescribed [...] Read more.
Nineteen fungal strains associated with the seagrass Posidonia oceanica, with the green alga Flabellia petiolata, and the brown alga Padina pavonica were collected in the Mediterranean Sea. These strains were previously identified at the family level and hypothesised to be undescribed species. Strains were examined by deep multi-loci phylogenetic and morphological analyses. Maximum-likelihood and Bayesian phylogenies proved that Parathyridariella gen. nov. is a distinct genus in the family Thyriadriaceae. Analyses based on five genetic markers revealed seven new species: Neoroussoella lignicola sp. nov., Roussoella margidorensis sp. nov., R. mediterranea sp. nov., and R. padinae sp. nov. within the family Roussellaceae, and Parathyridaria flabelliae sp. nov., P. tyrrhenica sp. nov., and Parathyridariella dematiacea gen. nov. et sp. nov. within the family Thyridariaceae. Full article
(This article belongs to the Special Issue Fungal Diversity in the Mediterranean Area)
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18 pages, 1275 KiB  
Article
Balkan Chamois (Rupicapra rupicapra balcanica) Avoids Roads, Settlements, and Hunting Grounds: An Ecological Overview from Timfi Mountain, Greece
by Vassiliki Kati, Christina Kassara, Dimitrios Vassilakis and Haritakis Papaioannou
Diversity 2020, 12(4), 124; https://doi.org/10.3390/d12040124 - 27 Mar 2020
Cited by 13 | Viewed by 7109
Abstract
Balkan chamois (Rupicapra rupicapra balcanica) is a protected species with an Inadequate-Bad (U2) conservation status in Greece. Our study explores its seasonal range use pattern, demography and habitat selection in a site of the Natura 2000 network, Timfi Mountain. To this [...] Read more.
Balkan chamois (Rupicapra rupicapra balcanica) is a protected species with an Inadequate-Bad (U2) conservation status in Greece. Our study explores its seasonal range use pattern, demography and habitat selection in a site of the Natura 2000 network, Timfi Mountain. To this aim, we examined 1168 observations obtained from six seasonal surveys (2002: four seasons, 2014 and 2017: autumn) and performed an ecological-niche factor analysis (ENFA), using 16 environmental and human-disturbance variables. The species had an annual range of 6491 ha (25% of the study area), followed the typical range-use pattern, and presented the minimum core area during the rutting season (autumn). Timfi Mt hosted 469 individuals in 2017 (the largest population in Greece), increasing by 3.55 times since 2002. The species selected higher altitudes during summer and autumn, pinewoods over broad-leaved woods as winter grounds, and it avoided south-facing slopes. Our results supported the anthropogenic risk avoidance hypothesis; the species always selected remote areas away from roads, human settlements, and hunting grounds. In Greece, 40% of its distribution area falls within hunting ban areas (16.5% of the country). A national conservation policy is needed towards maintaining and increasing roadless areas and hunting-ban areas within Balkan chamois range nationwide. Full article
(This article belongs to the Section Biodiversity Conservation)
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14 pages, 1590 KiB  
Article
Evidence for Plio-Pleistocene Duck Mussel Refugia in the Azov Sea River Basins
by Alena A. Tomilova, Artem A. Lyubas, Alexander V. Kondakov, Ilya V. Vikhrev, Mikhail Y. Gofarov, Yulia S. Kolosova, Maxim V. Vinarski, Dmitry M. Palatov and Ivan N. Bolotov
Diversity 2020, 12(3), 118; https://doi.org/10.3390/d12030118 - 23 Mar 2020
Cited by 25 | Viewed by 4483
Abstract
Freshwater mussels (Bivalvia: Unionoida) play an important role in freshwater habitats as ecosystem engineers of the water environment. Duck mussel Anodonta anatina is widely distributed throughout Europe, Siberia, and Western and Central Asia, which makes it a convenient object for biogeographic studies. In [...] Read more.
Freshwater mussels (Bivalvia: Unionoida) play an important role in freshwater habitats as ecosystem engineers of the water environment. Duck mussel Anodonta anatina is widely distributed throughout Europe, Siberia, and Western and Central Asia, which makes it a convenient object for biogeographic studies. In this study, we analyzed the divergence of A. anatina populations and discovered a separate genetic lineage distributed in rivers of the Azov Sea basin. This was confirmed by the high genetic distances between this group and previously defined populations, and by the position of this clade in the Bayesian phylogeny calibrated by an external substitution rate. Based on our approximate Bayesian computation (ABC) analysis, biogeographic scenarios of A. anatina dispersal in Europe and Northern, Western, and Central Asia over the Neogene–Quaternary were simulated. The haplogroup’s isolation in the rivers of the Azov Sea basin most likely occurred in the Late Pliocene that was probably facilitated by rearrangement of freshwater basins boundaries in the Ponto-Caspian Region. Population genetic indices show the stability of this group, which allowed it to exist in the river basins of the region for a long time. The discovery of a long-term refugium in the rivers of the Azov Sea led to a better understanding of freshwater fauna evolution in the Neogene–Quaternary and highlighted the importance of conservation of these freshwater animals in the region as a source of unique genetic diversity. Full article
(This article belongs to the Section Biodiversity Conservation)
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16 pages, 2120 KiB  
Article
Responses of Rotifer Community to Microhabitat Changes Caused by Summer-Concentrated Rainfall in a Shallow Reservoir, South Korea
by Jong-Yun Choi and Seong-Ki Kim
Diversity 2020, 12(3), 113; https://doi.org/10.3390/d12030113 - 21 Mar 2020
Cited by 21 | Viewed by 3956
Abstract
Empirical studies suggest that the structural heterogeneity of aquatic ecosystem microhabitat is determined by the diversity and abundance of macrophytes. However, excessive accumulation of free-floating macrophytes on the water surface can reduce the biomass of submerged macrophytes, resulting in a relatively simplified habitat [...] Read more.
Empirical studies suggest that the structural heterogeneity of aquatic ecosystem microhabitat is determined by the diversity and abundance of macrophytes. However, excessive accumulation of free-floating macrophytes on the water surface can reduce the biomass of submerged macrophytes, resulting in a relatively simplified habitat structure. We hypothesized that heavy summer rainfall disrupts the growth of free-floating macrophytes covering much of the Jangcheok Reservoir’s water surface, thereby resulting in a more complex habitat structure by allowing development of a more diverse of macrophytic community. We divided long-term (2008–2017) monitoring data (rainfall, macrophytes, and rotifers) into two groups: Rainy and Dry years, corresponding to years with annual rainfall higher and lower than the total annual average, respectively. We found that summer densities of rotifers fell sharply in Rainy years, but increased continuously in Dry years. This trend resulted in greater autumn densities in Rainy relative to Dry years, which we attributed to changes in habitat related to differential macrophyte development. Moderate disturbance of the water surface caused by high summer rainfall can promote growth of submerged macrophytes by creating large areas of open water and therefore a more complex autumnal microhabitat structure, resulting in seasonal variations in rotifer community structures and populations. Moreover, a highly complex microhabitat structure restricts foraging activity of fish (i.e., Lepomis macrochirus) that prey on rotifers. Based on these findings, we suggest that summer-concentrated rainfall plays an important role in supporting the density and species diversity of rotifers. Full article
(This article belongs to the Section Biodiversity Loss & Dynamics)
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22 pages, 6563 KiB  
Article
New Records of Antarctic Tardigrada with Comments on Interpopulation Variability of the Paramacrobiotus fairbanksi Schill, Förster, Dandekar and Wolf, 2010
by Łukasz Kaczmarek, Monika Mioduchowska, Uroš Kačarević, Katarzyna Kubska, Ivan Parnikoza, Bartłomiej Gołdyn and Milena Roszkowska
Diversity 2020, 12(3), 108; https://doi.org/10.3390/d12030108 - 20 Mar 2020
Cited by 27 | Viewed by 5059
Abstract
Studies on Antarctic tardigrades started at the beginning of the twentieth century and have progressed very slowly and ca. 75 tardigrade species are known from this region. Paramacrobiotus fairbanksi was described from USA based on genetic markers and later reported from Italy, Poland, [...] Read more.
Studies on Antarctic tardigrades started at the beginning of the twentieth century and have progressed very slowly and ca. 75 tardigrade species are known from this region. Paramacrobiotus fairbanksi was described from USA based on genetic markers and later reported from Italy, Poland, and Spain. The “everything is everywhere” hypothesis suggests that microscopic organisms have specific features which help them to inhabit most of environments and due to this they can be considered cosmopolitan. In the present paper, we report eight tardigrade taxa from Antarctic, including the first report of Pam. fairbanksi from Southern Hemisphere, which could suggest that the “everything is everywhere” hypothesis could be true, at least for some tardigrade species. Moreover, we also genetically and morphologically compare a few different populations of Pam. fairbanksi. The p-distances between COI haplotypes of all sequenced Pam. fairbanksi populations from Antarctica, Italy, Spain, USA and Poland ranged from 0.002% to 0.005%. In the case of COI polymorphism analyses, only one haplotype was observed in populations from Antarctica, USA and Poland, two haplotypes were found in population from Spain, and six haplotypes were observed in population from Italy. We also found some statistically significant morphometrical differences between the populations of Pam. fairbanksi from different regions and designed a new specific primers for Paramacrobiotus taxa. Full article
(This article belongs to the Special Issue Tardigrades Taxonomy, Biology and Ecology)
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10 pages, 287 KiB  
Article
Do Invasive Mosquito and Bird Species Alter Avian Malaria Parasite Transmission?
by Josué Martínez-de la Puente, Alazne Díez-Fernández, Tomás Montalvo, Rubén Bueno-Marí, Quentin Pangrani, Ramón C. Soriguer, Juan Carlos Senar and Jordi Figuerola
Diversity 2020, 12(3), 111; https://doi.org/10.3390/d12030111 - 20 Mar 2020
Cited by 20 | Viewed by 6099
Abstract
Alien mosquito and vertebrate host species may create novel epidemiological scenarios for the transmission of pathogens naturally circulating in the invaded area. The exotic Monk parakeet (Myiopsitta monachus) has established populations in Europe and is currently considered an invasive pest. Due [...] Read more.
Alien mosquito and vertebrate host species may create novel epidemiological scenarios for the transmission of pathogens naturally circulating in the invaded area. The exotic Monk parakeet (Myiopsitta monachus) has established populations in Europe and is currently considered an invasive pest. Due to their high abundance in urban areas, Monk parakeets could be involved in the transmission of pathogens, potentially affecting wildlife and livestock. To test this hypothesis, we determined the prevalence and diversity of three vector-borne parasites, namely Plasmodium, Haemoproteus and Leucocytozoon, in Monk parakeets from Barcelona. Many areas of southern Europe shelter high densities of the invasive Asian tiger mosquito Aedes albopictus, which in addition to native mosquito species could affect the transmission of mosquito-borne parasites, such as avian Plasmodium. Thus, we also sampled mosquitoes in the area to trace their blood-feeding hosts and determine the presence of Plasmodium parasites. Monk parakeets were neither infected by Plasmodium nor by Haemoproteus parasites, and only five individuals (3.13%; n = 160) were infected by Leucocytozoon. Monk parakeets were bitten by Culiseta longiareolata and represented 9.5% of Culex pipiens blood meals. The invasive Ae. albopictus showed a clear anthropophilic feeding pattern, with humans dominating its diet. Three Plasmodium lineages were detected in pools of Cx pipiens. These results suggest that Plasmodium circulating in the area cannot develop in the invasive Monk parakeet, in spite of the relatively high fraction of native mosquito vectors feeding on this species in its invaded distribution range. Full article
(This article belongs to the Section Animal Diversity)
15 pages, 1960 KiB  
Article
Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers
by Davide Bianchi, Lucio Brancadoro and Gabriella De Lorenzis
Diversity 2020, 12(3), 103; https://doi.org/10.3390/d12030103 - 16 Mar 2020
Cited by 19 | Viewed by 6615
Abstract
Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping [...] Read more.
Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of individuals belonging to Vitis species not commonly used in the breeding programs, was genotyped using the 18k SNP genotyping array. SNP results were compared to the established SSR (Simple Sequence Repeat) markers in terms of heterozygosity and genetic structure of the core collection. Genotyping array has proved to be a valuable tool for genotyping of grapevine rootstocks, with more than 90% of SNPs successfully amplified. Structure analysis detected a high degree of admixed genotypes, supported by the complex genetic background of non-vinifera germplasm. Moreover, SNPs clearly differentiated non-vinifera and vinifera germplasm. These results represent a first step in studying the genetic diversity of non-conventional breeding material that will be used to select rootstocks with high tolerance to limiting environmental conditions. Full article
(This article belongs to the Section Plant Diversity)
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27 pages, 2576 KiB  
Article
Austrian COLOSS Survey of Honey Bee Colony Winter Losses 2018/19 and Analysis of Hive Management Practices
by Hannes Oberreiter and Robert Brodschneider
Diversity 2020, 12(3), 99; https://doi.org/10.3390/d12030099 - 13 Mar 2020
Cited by 33 | Viewed by 8049
Abstract
We conducted a citizen science survey on overwinter honey bee colony losses in Austria. A total of 1534 beekeepers with 33,651 colonies reported valid loss rates. The total winter loss rate for Austria was 15.2% (95% confidence interval: 14.4–16.1%). Young queens showed a [...] Read more.
We conducted a citizen science survey on overwinter honey bee colony losses in Austria. A total of 1534 beekeepers with 33,651 colonies reported valid loss rates. The total winter loss rate for Austria was 15.2% (95% confidence interval: 14.4–16.1%). Young queens showed a positive effect on colony survival and queen-related losses. Observed queen problems during the season increased the probability of losing colonies to unsolvable queen problems. A notable number of bees with crippled wings during the foraging season resulted in high losses and could serve as an alarm signal for beekeepers. Migratory beekeepers and large operations had lower loss rates than smaller ones. Additionally, we investigated the impact of several hive management practices. Most of them had no significant effect on winter mortality, but purchasing wax from outside the own operation was associated with higher loss rates. Colonies that reported foraging on maize and late catch crop fields or collecting melezitose exhibited higher loss rates. The most common Varroa destructor control methods were a combination of long-term formic acid treatment in summer and oxalic acid trickling in winter. Biotechnical methods in summer had a favourable effect on colony survival. Full article
(This article belongs to the Special Issue Monitoring of Honey Bee Colony Losses)
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