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Diversity, Volume 11, Issue 9 (September 2019)

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Cover Story (view full-size image) We combined anatomical and genomic data to resolve the contentious phylogenetic relationships among [...] Read more.
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Open AccessArticle
Back from the Past: DNA Barcodes and Morphology Support Ablabesmyia americana Fittkau as a Valid Species (Diptera: Chironomidae)
Diversity 2019, 11(9), 173; https://doi.org/10.3390/d11090173 - 19 Sep 2019
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Abstract
Short, standardized gene fragments for species identification (DNA barcodes) have proven effective in delineating closely-related insect species, and can be critical characters to include in taxonomic studies. This is also the case for the species-rich and widely distributed fly family Chironomidae (non-biting midges). [...] Read more.
Short, standardized gene fragments for species identification (DNA barcodes) have proven effective in delineating closely-related insect species, and can be critical characters to include in taxonomic studies. This is also the case for the species-rich and widely distributed fly family Chironomidae (non-biting midges). Inspired by observed genetic differences in partial COI gene sequences between North American and European populations of the chironomid Ablabesmyia monilis sensu lato, we investigated whether or not the morphology of male and female adults supported the distinction of more than one species. Our results support that the junior synonym Ablabesmyia americana is a valid species separate from A. monilis, and that A. monilis sensu stricto is distributed both in the Palearctic region and in North America. We provide re-descriptions of all of the major life stages of A. americana and of the adult female of A. monilis. Full article
(This article belongs to the Section Animal Diversity)
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Open AccessArticle
The Fate of Endangered Rock Sedge (Carex rupestris) in the Western Carpathians—The Future Perspective of an Arctic-Alpine Species under Climate Change
Diversity 2019, 11(9), 172; https://doi.org/10.3390/d11090172 - 19 Sep 2019
Viewed by 290
Abstract
Carex rupestris is an endangered and rare arctic-alpine element of the Western Carpathian flora. Given the geographically isolated and spatially restricted peripheral ranges of arctic-alpine species, there is a good chance that many species of conservation concern irreversibly disappear from the regional flora [...] Read more.
Carex rupestris is an endangered and rare arctic-alpine element of the Western Carpathian flora. Given the geographically isolated and spatially restricted peripheral ranges of arctic-alpine species, there is a good chance that many species of conservation concern irreversibly disappear from the regional flora under the ongoing climate change. In this study, we gathered all existing data on the presence of C. rupestris and focused on its current and future distribution in the Western Carpathians. We found that although the distribution of the species is fragmented and scarce, C. rupestris occurs in several mountain ranges, in four distinct plant community types, which differ considerably in altitude, geological bedrock, and other habitat characteristics. In contrast to the relatively broad range of occupied habitats, C. rupestris shows a narrow temperature niche (mean annual temperature range 0.4–4.0 °C). Ensembles of small models based on climatic characteristics and local topography show that regardless of the climate change scenario (rcp2.6, rcp8.5), many current occurrence sites, mainly in the peripheral zones of the range, will face the excessive loss of suitable environmental conditions. It is expected that the Tatra Mountains will be the only mountain range retaining potentially suitable habitats and providing possible refugia for this cold-adapted species in the future. Such severe shrinkage of distribution ranges and associated geographic isolation raises serious concerns for the fate of the arctic-alpine species in the Western Carpathians. Full article
(This article belongs to the Section Plant Diversity)
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Open AccessEditorial
Lichen Diversity and Biomonitoring: A Special Issue
Diversity 2019, 11(9), 171; https://doi.org/10.3390/d11090171 - 18 Sep 2019
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Abstract
Lichens are symbiotic organisms susceptible to environmental alteration due to their morphological and physiological features. For this reason, researchers and decision-makers are extensively using lichen biomonitoring for assessing the effects of various anthropogenic disturbances. The Special Issue was launched to fulfil some knowledge [...] Read more.
Lichens are symbiotic organisms susceptible to environmental alteration due to their morphological and physiological features. For this reason, researchers and decision-makers are extensively using lichen biomonitoring for assessing the effects of various anthropogenic disturbances. The Special Issue was launched to fulfil some knowledge gaps in this field, such as the development of procedures to interpret and compare results. The SI includes three reviews that explore the application of lichen biomonitoring for detecting the effects of climate change. Three articles and one review paper examined the use at a decision level of biomonitoring of air pollution employing lichens, including the application in environmental forensic. Finally, six research articles are illustrative examples of lichen biomonitoring in poorly known habitats, providing data from the physiological to the community level of observation, and pose the basis for extending comparable approaches on a global scale. Full article
(This article belongs to the Special Issue Lichen Diversity and Biomonitoring)
Open AccessArticle
First Survey of Heterobranch Sea Slugs (Mollusca, Gastropoda) from the Island Sangihe, North Sulawesi, Indonesia
Diversity 2019, 11(9), 170; https://doi.org/10.3390/d11090170 - 17 Sep 2019
Viewed by 307
Abstract
Indonesia is famous for its underwater biodiversity, which attracts many tourists, especially divers. This is also true for Sangihe Islands Regency, an area composed of several islands in the northern part of North Sulawesi. However, Sangihe Islands Regency is much less known than, [...] Read more.
Indonesia is famous for its underwater biodiversity, which attracts many tourists, especially divers. This is also true for Sangihe Islands Regency, an area composed of several islands in the northern part of North Sulawesi. However, Sangihe Islands Regency is much less known than, e.g., Bunaken National Park (BNP, North Sulawesi). The main island, Sangihe, has recently experienced an increase in tourism and mining activities with potentially high impact on the environment. Recently, monitoring projects began around BNP using marine Heterobranchia as indicators for coral reef health. No information about this taxon exists from the remote islands in North Sulawesi. The present study represents the first monitoring study ever and focuses on marine Heterobranchia around Sangihe. In total, 250 specimens were collected, which could be assigned to Sacoglossa (3), Anthobranchia (19), and Cladobranchia (1). Despite the low number (23 versus 172 in BNP), at least eight species (35%) are not recorded from BNP, probably indicating differences in habitat, but also influence of a strong El Niño year in 2016. Here we also report for the first time a Chromodoris annae specimen mimicking C. elisabethina, and the discovery of a new Phyllidia species. Full article
(This article belongs to the Section Marine Diversity)
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Open AccessArticle
Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order
Diversity 2019, 11(9), 169; https://doi.org/10.3390/d11090169 - 17 Sep 2019
Viewed by 365
Abstract
Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates [...] Read more.
Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Arthropods)
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Open AccessReview
Role of Reef-Building, Ecosystem Engineering Polychaetes in Shallow Water Ecosystems
Diversity 2019, 11(9), 168; https://doi.org/10.3390/d11090168 - 17 Sep 2019
Viewed by 235
Abstract
Although the effect of ecosystem engineers in structuring communities is common in several systems, it is seldom as evident as in shallow marine soft-bottoms. These systems lack abiotic three-dimensional structures but host biogenic structures that play critical roles in controlling abiotic conditions and [...] Read more.
Although the effect of ecosystem engineers in structuring communities is common in several systems, it is seldom as evident as in shallow marine soft-bottoms. These systems lack abiotic three-dimensional structures but host biogenic structures that play critical roles in controlling abiotic conditions and resources. Here I review how reef-building polychaetes (RBP) engineer their environment and affect habitat quality, thus regulating community structure, ecosystem functioning, and the provision of ecosystem services in shallow waters. The analysis focuses on different engineering mechanisms, such as hard substrate production, effects on hydrodynamics, and sediment transport, and impacts mediated by filter feeding and biodeposition. Finally, I deal with landscape-level topographic alteration by RBP. In conclusion, RBP have positive impacts on diversity and abundance of many species mediated by the structure of the reef. Additionally, by feeding on phytoplankton and decreasing water turbidity, RBP can control primary production, increase light penetration, and might alleviate the effects of eutrophication affecting supporting ecosystem services, such as nutrient cycling. They can also modulate cultural ecosystem services by affecting recreational activities (e.g., negative impacts on boating and angling, increased value of sites as birdwatching sites). Acknowledging the multiplicity of synergistic and antagonistic effects of RBP on ecosystems and linking changes in habitat structure, filter-feeding activities, and biodeposition to ecosystem services are essential for effective decision-making regarding their management and restoration. Full article
(This article belongs to the Special Issue Diversity of Ecosystem Engineers in the World Coasts and Oceans)
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Open AccessArticle
Interannual Variation of Benthic Macroinvertebrate Communities at Long-Term Monitoring Sites Impacted by Human Activities: Implications for Bioassessment
Diversity 2019, 11(9), 167; https://doi.org/10.3390/d11090167 - 16 Sep 2019
Viewed by 328
Abstract
Bioassessment assumes that ecological conditions remain stable in the absence of environmental changes. Evidence suggests this assumption may hold for reference streams, but knowledge gaps remain for impacted streams. Our study quantified interannual variation of benthic macroinvertebrate communities, monitored for at least 14 [...] Read more.
Bioassessment assumes that ecological conditions remain stable in the absence of environmental changes. Evidence suggests this assumption may hold for reference streams, but knowledge gaps remain for impacted streams. Our study quantified interannual variation of benthic macroinvertebrate communities, monitored for at least 14 years in eight impacted streams in the Upper Thames River watershed in Ontario, Canada. Benthic communities exhibited moderate interannual variation in relative abundance of EPT (Ephemeroptera, Plecoptera and Trichoptera) and Chironomidae taxa. Year-to-year changes were reflected in lower community persistence than that observed in studies of reference streams. In contrast, tolerance-based metrics showed minimal interannual variation, suggesting compositional changes were because of taxonomic substitutions, in which one tolerant taxon replaced another. Analyses indicated limited directionality in temporal variation for most bioassessment metrics. An exception was taxa richness, which increased at most sites, possibly because of changes in subsampling. However, no associations between calculated bioassessment metrics and measured environmental factors (stream flow and water chemistry) or sampling procedures were observed. We conclude interannual variation in ecological conditions can be substantial and may not be associated with deterministic factors routinely measured in stream assessments. We recommend increased sampling frequency and traits-based assessment as options for limiting effects of interannual variation on assessment results. Full article
(This article belongs to the Special Issue Aquatic Environmental Monitoring and Assessment)
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Open AccessArticle
The Influential Role of the Habitat on the Diversity Patterns of Free-Living Aquatic Nematode Assemblages in the Cuban Archipelago
Diversity 2019, 11(9), 166; https://doi.org/10.3390/d11090166 - 16 Sep 2019
Viewed by 276
Abstract
Free living nematodes are the most abundant and diverse metazoans in aquatic sediments. We used a framework of habitat types to reveal quantitative patterns in species richness (SR), β-diversity, and biological traits (BT). Meiofauna was quantitatively collected from 60 sites within nine habitat [...] Read more.
Free living nematodes are the most abundant and diverse metazoans in aquatic sediments. We used a framework of habitat types to reveal quantitative patterns in species richness (SR), β-diversity, and biological traits (BT). Meiofauna was quantitatively collected from 60 sites within nine habitat types and 24,736 nematodes were identified to species level. We reported a regional richness of 410 ± 12 species for the Cuban archipelago; however, caves and deep waters need to be sampled more intensively. Relationships between SR and abundance supported the dynamic equilibrium model with habitats ordered across gradients of resource availability and physical disturbance. Seagrass meadows were the most specious and freshwater/anchihaline caves the least diverse habitats. Differences in β-diversity likely were due to habitat heterogeneity and limitations for dispersal. The assemblage composition was unique in some habitats likely reflecting the effects of habitat filtering. However, coastal habitats shared many species reflecting high connectivity and dispersal capability of nematodes due to hydrodynamics. The BTs “life strategy”, “trophic group”, and “tail shape” reflected ecological adaptations; but “amphidial fovea” and “cuticle”, likely reflected phylogenetic signatures from families/genera living in different habitats. Habitat type played an influential role in the diversity patterns of aquatic nematodes from taxonomic and functional points of view. Full article
(This article belongs to the Special Issue Meiofauna Biodiversity and Ecology)
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Open AccessArticle
What is the Long-Term Effect of Bamboo Dominance on Adult Trees in the Araucaria Forest? A Comparative Analysis between Two Successional Stages in Southern Brazil
Diversity 2019, 11(9), 165; https://doi.org/10.3390/d11090165 - 16 Sep 2019
Viewed by 395
Abstract
Bamboos are opportunistic species that rapidly colonize open areas following forest disturbance, forming dense clusters that alter the regenerative processes and maintain lower levels of tree diversity. Widespread forest degradation, especially in Latin America and Asia, and human-induced introduction have allowed native and [...] Read more.
Bamboos are opportunistic species that rapidly colonize open areas following forest disturbance, forming dense clusters that alter the regenerative processes and maintain lower levels of tree diversity. Widespread forest degradation, especially in Latin America and Asia, and human-induced introduction have allowed native and non-native bamboo species to thrive, hindering successional pathways that would otherwise lead to more diverse forests; such a large-scale phenomenon is a key concern in the conservation of forest resources around the globe. Despite previous research on this phenomenon, little is known about the long-term effects of bamboo dominance on forest structure and composition and the corresponding interaction with natural regeneration. As such, we sought to evaluate the long-term effects of bamboo dominance on the dynamics of adult forest populations considering two forest types (Bamboo Forest—BF and Araucaria Forest—AF) over an 11-year period in the Embrapa Research Station in Caçador, Brazil. We monitored 20 plots (15 × 15 m) in each forest type where we tagged, identified, and measured the height and diameter of all the trees taller than 1.5 m (H) and diameter at breast height (DBH) greater than 3.18 cm. Comparisons were based on forest species diversity and structure parameters. In BF, diversity of species increased after the bamboo die-off that occurred in 2006 with a subsequent reduction in the number of pioneer species overtime. However, secondary species remained stagnant demonstrating that recruitment and transition into higher size classes is restricted to the immediate die-off aftermath. On the other hand, plant diversity and structure in the relatively bamboo-free AF were stable with secondary species accounting for the most richness. Our results confirm that BF maintains significantly lower levels of diversity that are restricted to pioneer species; AF structure and diversity are not significantly affected by bamboo die-off and recolonization; and BF tree species are caught in a closed cycle of arrested successional development. The widespread presence of bamboos as dominant species in the region should become a part of the conversation pertaining to forest management and conservation in Brazil and other countries in south America and Asia. Full article
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Open AccessArticle
Potential Invasion Risk of Pet Traded Lizards, Snakes, Crocodiles, and Tuatara in the EU on the Basis of a Risk Assessment Model (RAM) and Aquatic Species Invasiveness Screening Kit (AS-ISK)
Diversity 2019, 11(9), 164; https://doi.org/10.3390/d11090164 - 13 Sep 2019
Viewed by 242
Abstract
Because biological invasions can cause many negative impacts, accurate predictions are necessary for implementing effective restrictions aimed at specific high-risk taxa. The pet trade in recent years became the most important pathway for the introduction of non-indigenous species of reptiles worldwide. Therefore, we [...] Read more.
Because biological invasions can cause many negative impacts, accurate predictions are necessary for implementing effective restrictions aimed at specific high-risk taxa. The pet trade in recent years became the most important pathway for the introduction of non-indigenous species of reptiles worldwide. Therefore, we decided to determine the most common species of lizards, snakes, and crocodiles traded as pets on the basis of market surveys in the Czech Republic, which is an export hub for ornamental animals in the European Union (EU). Subsequently, the establishment and invasion potential for the entire EU was determined for 308 species using proven risk assessment models (RAM, AS-ISK). Species with high establishment potential (determined by RAM) and at the same time with high potential to significantly harm native ecosystems (determined by AS-ISK) included the snakes Thamnophis sirtalis (Colubridae), Morelia spilota (Pythonidae) and also the lizards Tiliqua scincoides (Scincidae) and Intellagama lesueurii (Agamidae). Full article
(This article belongs to the Special Issue Biological Invasions 2020 Horizon)
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Open AccessArticle
Stable Isotope Analyses of Multiple Tissues of Great Shearwaters (Ardenna Gravis) Reveals Long-Term Dietary Stability, Short-Term Changes in Diet, and Can be Used as a Tool to Monitor Food Webs
Diversity 2019, 11(9), 163; https://doi.org/10.3390/d11090163 - 12 Sep 2019
Viewed by 502
Abstract
The great shearwater (Ardenna gravis) is a common pelagic bird with a distribution that spans almost the entire Atlantic basin, which in conjunction with its relatively high abundance, makes great shearwaters an effective bio indicator. We compared δ13C and [...] Read more.
The great shearwater (Ardenna gravis) is a common pelagic bird with a distribution that spans almost the entire Atlantic basin, which in conjunction with its relatively high abundance, makes great shearwaters an effective bio indicator. We compared δ13C and δ15N values from the feathers, red blood cells (RBCs), and plasma of great shearwaters collected in 2014 and 2015 from the waters off Massachusetts and Cape Cod. The δ13C and δ15N values of RBCs were quite constant between sampling periods and years, suggesting a generally stable food web over that time period. However, the δ13C of plasma indicates a small seasonal change in diet between July and September for both years, with plasma δ15N values suggesting a slight increase in trophic level late in summer. Comparison of the δ15N of RBCs and plasma indicates that great shearwaters experienced a diet shift during the first few weeks of summer 2014, but not in 2015. Comparisons with other studies suggest that these shearwaters feed at a lower trophic level than great shearwaters sampled in the Bay of Fundy and that there is a decrease in δ13C with increasing latitude, which could indicate a more pelagic diet in northern waters. Stable isotope analysis of the sixth primary feathers provided evidence that these feathers are molted in the Northern Hemisphere and that the diet of great shearwaters shortly after arrival was different in 2014 and 2015. This study demonstrates that within species comparisons of tissue isotopic signatures over time and comparisons of isotopic signatures of tissues with different turnover rates, can detect changes in diet and be used as a tool to monitor for changes in marine food webs over time and space. The relevant signals remain informative even in the absence of species-specific data on tissue-diet discrimination factors, tissue turnover rates, or knowledge of dietary components and their stable isotopic signatures, suggesting dietary changes indicative of a corresponding change in the food web. Full article
(This article belongs to the Special Issue Stable Isotopes in Ecological Research)
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Open AccessArticle
The Invasive Niche, a Multidisciplinary Concept Illustrated by Gorse (Ulex Europaeus)
Diversity 2019, 11(9), 162; https://doi.org/10.3390/d11090162 - 12 Sep 2019
Viewed by 230
Abstract
This study analyzes the natural and social factors influencing the emergence and publicization of the invasive status of a fast-growing bush, gorse (Ulex europaeus), by comparison between countries on a global scale. We used documents collected on the web in a [...] Read more.
This study analyzes the natural and social factors influencing the emergence and publicization of the invasive status of a fast-growing bush, gorse (Ulex europaeus), by comparison between countries on a global scale. We used documents collected on the web in a standardized way. The results show that in all the countries studied, there are several public statuses attributed to gorse. The invasive status is the one that is most shared. The other most frequently encountered status are those of noxious weed, and those of which are economically useful. The invasive status is publicized in nearly all countries, including those where gorse is almost absent. We quantified the publicization of the invasive gorse status of gorse by an indicator with 5 levels, and then performed a multivariate analysis that combines natural and social explanatory variables. The results lead us to propose the concept of invasive niche, which is the set of natural and social parameters that allow a species to be considered invasive in a given socio-ecosystem Full article
(This article belongs to the Special Issue Biological Invasions 2020 Horizon)
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Open AccessArticle
Three New Lizard Species of the Liolaemus montanus Group from Perú
Diversity 2019, 11(9), 161; https://doi.org/10.3390/d11090161 - 11 Sep 2019
Viewed by 1047
Abstract
Three new species of Liolaemus belonging to the L. montanus group are described from Perú. Two new species are restricted to the Ica and Moquegua departments on the Pacific coast, and one new species is only known from an isolated highland in Ayacucho [...] Read more.
Three new species of Liolaemus belonging to the L. montanus group are described from Perú. Two new species are restricted to the Ica and Moquegua departments on the Pacific coast, and one new species is only known from an isolated highland in Ayacucho department. These three new species differ from closely related species in their coloration patterns and head shape. We comment on the conservation issues of the new species and other Peruvian species of the L. montanus group. Full article
(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)
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Open AccessArticle
Influence of Forest Structure and Composition on Summer Habitat Use of Wildlife in an Upland Hardwood Forest
Diversity 2019, 11(9), 160; https://doi.org/10.3390/d11090160 - 08 Sep 2019
Viewed by 400
Abstract
Oak-hickory (Quercus-Carya spp.) forest types are widespread across the midwestern United States, but changes in forest disturbance regimes are resulting in little to no oak recruitment and a compositional shift to shade-tolerant, mesophytic species, such as American beech (Fagus grandifolia) [...] Read more.
Oak-hickory (Quercus-Carya spp.) forest types are widespread across the midwestern United States, but changes in forest disturbance regimes are resulting in little to no oak recruitment and a compositional shift to shade-tolerant, mesophytic species, such as American beech (Fagus grandifolia) and sugar maple (Acer saccharum). We conducted camera trap surveys in a mature upland hardwood forest of southern Illinois, USA during May to August 2015–2016 to document mammal summer habitat use in relation to forest structure and composition to further understand how regional shifts in forests may affect mammal communities. With nearly 4000 camera days of effort, we modeled occupancy patterns for white-tailed deer (Odocoileus virginianus), raccoon (Procyon lotor), and eastern gray squirrel (Sciurus canadensis). Forest composition models outcompeted forest structure models for white-tailed deer, where we observed a statistically significant negative relationship between white-tailed deer habitat use and beech dominance. Further, we found a strong, positive association between deer and oak dominance. Model selection indicated little support for within-stand forest structure or composition characteristics influencing habitat use for raccoons. Eastern gray squirrel occurrence was best described by forest composition, revealing a positive relationship with beech–maple importance values. Our predictive models indicated that the impact of forest changes underway will have varying impacts on wildlife species. We can expect changes in habitat use patterns to be more pronounced with time barring revised forest management practices, and these changes are likely to be most influential at the landscape-scale. We conclude that a patchwork mosaic of forest conditions will likely best support a diverse and abundant mammal community across the region. Full article
(This article belongs to the Section Animal Diversity)
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Open AccessArticle
Activity Patterns of Cave-Dwelling Bat Species during Pre-Hibernation Swarming and Post-Hibernation Emergence in the Central Appalachians
Diversity 2019, 11(9), 159; https://doi.org/10.3390/d11090159 - 06 Sep 2019
Viewed by 312
Abstract
In North America, bat research efforts largely have focused on summer maternity colonies and winter hibernacula, leaving the immediate pre- and post-hibernation ecology for many species unstudied. Understanding these patterns and processes is critical for addressing potential additive impacts to White-nose Syndrome (WNS)-affected [...] Read more.
In North America, bat research efforts largely have focused on summer maternity colonies and winter hibernacula, leaving the immediate pre- and post-hibernation ecology for many species unstudied. Understanding these patterns and processes is critical for addressing potential additive impacts to White-nose Syndrome (WNS)-affected bats, as autumn is a time of vital weight gain and fat resources are largely depleted in early spring in surviving individuals. Our study sought to examine autumn and spring bat activity patterns in the central Appalachian Mountains around three hibernacula to better understand spatio-temporal patterns during staging for hibernation and post-hibernation migration in the post-WNS environment. From early September through November 2015 and 2016, and from early March through April 2016 and 2017, we assessed the effects of distance to hibernacula and ambient conditions on nightly bat activity for Myotis spp. and big brown bats (Eptesicus fuscus) using zero-crossing frequency division bat detectors near cave entrances and 1 km, 2 km, and 3 km distant from caves. Following identification of echolocation calls, we used generalized linear mixed effects models to examine patterns of activity across the landscape over time and relative to weather. Overall bat activity was low at all sample sites during autumn and spring periods except at sites closest to hibernacula. Best-supported models describing bat activity varied, but date and ambient temperatures generally appeared to be major drivers of activity in both seasons. Total activity for all species had largely ceased by mid-November. Spring bat activity was variable across the sampling season, however, some activity was observed as early as mid-March, almost a month earlier than the historically accepted emergence time regionally. Current timing of restrictions on forest management activities that potentially remove day-roosts near hibernacula when bats are active on the landscape may be mismatched with actual spring post-hibernation emergence. Adjustments to the timing of these restrictions during the spring may help to avoid potentially additive negative impacts on WNS-impacted bat species. Full article
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Open AccessArticle
Inventory and Historical Changes in the Marine Flora of Tomioka Peninsula (Amakusa Island), Japan
Diversity 2019, 11(9), 158; https://doi.org/10.3390/d11090158 - 06 Sep 2019
Viewed by 448
Abstract
Intensive algal sampling was conducted from 2012 to 2017 in the Tomioka Peninsula, Amakusa-Shimoshima Island (the East China Sea, Japan), yielding a total of 293 benthic macroalgal taxa, of which 63% were red algae, 16% were brown algae, and 19% were green algae. [...] Read more.
Intensive algal sampling was conducted from 2012 to 2017 in the Tomioka Peninsula, Amakusa-Shimoshima Island (the East China Sea, Japan), yielding a total of 293 benthic macroalgal taxa, of which 63% were red algae, 16% were brown algae, and 19% were green algae. The majority (69%) of species were previously recorded only for the tropics and/or subtropics, whereas 31% of species were recorded for temperate latitudes. Among all species of algae found from 2012 to 2017 in the Tomioka Peninsula, 163 species (56%) were newly identified species for Amakusa-Shimoshima Island, including six taxa, which were recorded in Japan for the first time. Comparison of the current data from the Amakusa-Shimoshima Island with those of nearby tropical regions suggested that the recent marine flora of the Amakusa-Shimoshima Island was more closely affiliated with the flora of a warm-temperate region. Moreover, we found that the benthic flora of the Tomioka Peninsula was significantly changed between the 1950s (Segawa & Yoshida 1961) and 2012–2017. For example, the species diversity was increased by two times, mainly at the expense of red and green algae, and the biogeographic status of the benthic flora was changed from the flora of a cold-temperate region to the flora of a warm-temperate region, which could be attributed to an introduction of red algae from the tropics of South East Asia and widespread opportunistic green algae, as well as the disappearance of cold-water brown algae. Collectively, our data suggested that these changes were driven by the global warming effect on the ocean. Full article
(This article belongs to the Special Issue Biodiversity of Macroalgae)
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Open AccessArticle
Are Wildland Fires Increasing Large Patches of Complex Early Seral Forest Habitat?
Diversity 2019, 11(9), 157; https://doi.org/10.3390/d11090157 - 06 Sep 2019
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Abstract
High-severity fire creates patches of complex early seral forest (CESF) in mixed-severity fire complexes of the western USA. Some managers and researchers have expressed concerns that large high-severity patches are increasing and could adversely impact old forest extent or lead to type conversions. [...] Read more.
High-severity fire creates patches of complex early seral forest (CESF) in mixed-severity fire complexes of the western USA. Some managers and researchers have expressed concerns that large high-severity patches are increasing and could adversely impact old forest extent or lead to type conversions. We used GIS databases for vegetation and fire severity to investigate trends in large (>400 ha) CESF patches in frequent-fire forests of the western USA, analyzing four equal time periods from 1984 to 2015. We detected a significant increase in the total area of large patches relative to the first time period only (1984–1991), but no significant upward trend since the early 1990s. There was no significant trend in the size of large CESF patches between 1984 and 2015. Fire rotation intervals for large CESF patches ranged from ~12 centuries to over 4000 years, depending on the region. Large CESF patches were highly heterogeneous, internally creating ample opportunities for fire-mediated biodiversity. Interior patch areas far removed from the nearest low/moderate-severity edges comprised a minor portion of high-severity patches but may be ecologically important in creating pockets of open forest. There was ample historical evidence of large CESF patches but no evidence of increases that might indicate a current risk of ecosystem-type shifts. Full article
(This article belongs to the Section Animal Diversity)
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Open AccessReview
Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy
Diversity 2019, 11(9), 156; https://doi.org/10.3390/d11090156 - 05 Sep 2019
Viewed by 298
Abstract
Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant [...] Read more.
Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes. Full article
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Open AccessReview
Principles and Challenges for Multi-Stakeholder Development of Focused, Tiered, and Triggered, Adaptive Monitoring Programs for Aquatic Environments
Diversity 2019, 11(9), 155; https://doi.org/10.3390/d11090155 - 04 Sep 2019
Viewed by 287
Abstract
In Canada, there is almost 30 years of experience in developing tiered and triggered adaptive monitoring programs focused on looking at whether environmental concerns remain when pulp and paper mills, or metal mines, are in compliance with their discharge limits. These environmental effects [...] Read more.
In Canada, there is almost 30 years of experience in developing tiered and triggered adaptive monitoring programs focused on looking at whether environmental concerns remain when pulp and paper mills, or metal mines, are in compliance with their discharge limits. These environmental effects monitoring programs were based on nationally standardized designs. Many of the programs have been developed through multi-stakeholder working groups, and the evolution of the program faced repeated frictions and differing opinions on how to design environmental monitoring programs. This paper describes key guidance to work through the initial steps in program design, and includes scientific advice based on lessons learned from the development of the Canadian aquatic environmental effects monitoring program. Full article
(This article belongs to the Special Issue Aquatic Environmental Monitoring and Assessment)
Open AccessArticle
Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces
Diversity 2019, 11(9), 154; https://doi.org/10.3390/d11090154 - 03 Sep 2019
Viewed by 323
Abstract
The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material [...] Read more.
The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation. Full article
(This article belongs to the Section Plant Diversity)
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Open AccessArticle
Phylogeny and Biogeography of Branchipolynoe (Polynoidae, Phyllodocida, Aciculata, Annelida), with Descriptions of Five New Species from Methane Seeps and Hydrothermal Vents
Diversity 2019, 11(9), 153; https://doi.org/10.3390/d11090153 - 31 Aug 2019
Viewed by 448
Abstract
The four named species of Branchipolynoe all live symbiotically in mytilid mussels (Bathymodiolus) that occur at hydrothermal vents or methane seeps. Analyses using mitochondrial (COI and 16S) and nuclear (ITS) genes, as well as morphology, were conducted on a collection of [...] Read more.
The four named species of Branchipolynoe all live symbiotically in mytilid mussels (Bathymodiolus) that occur at hydrothermal vents or methane seeps. Analyses using mitochondrial (COI and 16S) and nuclear (ITS) genes, as well as morphology, were conducted on a collection of Branchipolynoe from Pacific Costa Rican methane seeps and West Pacific hydrothermal vents. This revealed five new species of Branchipolynoe, and these are formally described. The new species from Costa Rica live in three species of Bathymodiolus mussels (also new) at depths ranging from 1000 to 1800 m. Branchipolynoe kajsae n. sp. and Branchipolynoe halliseyae n. sp. were found in all three undescribed Bathymodiolus species, while Branchipolynoe eliseae n. sp. was found in Bathymodiolus spp. 1 and 2, and Branchipolynoe meridae n. sp. was found in Bathymodiolus spp. 1 and 3. Hence, Bathymodiolus sp. 1 hosted all four of the new species, while the other two Bathymodiolus hosted three each. Most mussels contained only one specimen of Branchipolynoe; where there was more than one, these were often a female and smaller male of the same species. The newly discovered species from the West Pacific, Branchipolynoe tjiasmantoi n. sp., lives in unidentified Bathymodiolus at depths ranging from 674 to 2657 m from hydrothermal vents in the North Fiji (Fiji) and Lau Basins (Tonga) and also from New Zealand, Vanuatu, and the Manus Basin (Papua New Guinea). The phylogenetic and biogeographical implications of this diversity of Branchipolynoe are discussed. Full article
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Open AccessArticle
Barcoding Analysis of Paraguayan Squamata
Diversity 2019, 11(9), 152; https://doi.org/10.3390/d11090152 - 30 Aug 2019
Viewed by 421
Abstract
Paraguay is a key spot in the central region of South America where several ecoregions converge. Its fauna (and specifically its herpetofauna) is getting better studied than years before, but still there is a lack of information regarding molecular genetics, and barcoding analyses [...] Read more.
Paraguay is a key spot in the central region of South America where several ecoregions converge. Its fauna (and specifically its herpetofauna) is getting better studied than years before, but still there is a lack of information regarding molecular genetics, and barcoding analyses have proven to be an excellent tool in this matter. Here, we present results of a barcoding analysis based on 16S rRNA gene sequences, providing valuable data for the scientific community in the region. We based our fieldwork in several areas of Paraguay. We analyzed 249 samples (142 sequenced by us) with a final alignment of 615 bp length. We identified some taxonomic incongruences that can be addressed based on our results. Furthermore, we identify groups, where collecting efforts and research activities should be reinforced. Even though we have some blanks in the geographical coverage of our analysis—and there is still a lot to do towards a better understanding of the taxonomy of the Paraguayan herpetofauna—here, we present the largest genetic dataset for the mitochondrial DNA gene 16S of reptiles (particularly, Squamata) from Paraguay, which can be used to solve taxonomic problems in the region. Full article
(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)
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Open AccessArticle
Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies
Diversity 2019, 11(9), 151; https://doi.org/10.3390/d11090151 - 29 Aug 2019
Viewed by 526
Abstract
The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and [...] Read more.
The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group. Full article
(This article belongs to the Special Issue Biodiversity of Insect)
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Open AccessArticle
Conservation Status of Brachycephalus Toadlets (Anura: Brachycephalidae) from the Brazilian Atlantic Rainforest
Diversity 2019, 11(9), 150; https://doi.org/10.3390/d11090150 - 27 Aug 2019
Viewed by 725
Abstract
The number of described anurans has increased continuously, with many newly described species determined to be at risk. Most of these new species inhabit hotspots and are under threat of habitat loss, such as Brachycephalus, a genus of small toadlets that inhabits [...] Read more.
The number of described anurans has increased continuously, with many newly described species determined to be at risk. Most of these new species inhabit hotspots and are under threat of habitat loss, such as Brachycephalus, a genus of small toadlets that inhabits the litter of the Brazilian Atlantic Rainforest. Of 36 known species, 22 were described in the last decade, but only 11 have been assessed according to the IUCN Red List categories, with just one currently listed as Critically Endangered. All available data on occurrence, distribution, density, and threats to Brachycephalus were reviewed. The species extent of occurrence was estimated using the Minimum Convex Polygon method for species with three or more records and by delimiting continuous areas within the altitudinal range of species with up to two records. These data were integrated to assess the conservation status according to the IUCN criteria. Six species have been evaluated as Critically Endangered, five as Endangered, 10 as Vulnerable, five as Least Concern, and 10 as Data Deficient. Deforestation was the most common threat to imperiled Brachycephalus species. The official recognition of these categories might be more readily adopted if the microendemic nature of their geographical distribution is taken into account. Full article
(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)
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Open AccessArticle
Genetic Data Suggest Multiple Introductions of the Lionfish (Pterois miles) into the Mediterranean Sea
Diversity 2019, 11(9), 149; https://doi.org/10.3390/d11090149 - 27 Aug 2019
Viewed by 752
Abstract
Widespread reports over the last six years confirm the establishment of lionfish (Pterois miles) populations in the eastern Mediterranean. Accumulated knowledge on lionfish invasions in the western Atlantic Ocean has shown that it is a successful invader and can have negative impacts on [...] Read more.
Widespread reports over the last six years confirm the establishment of lionfish (Pterois miles) populations in the eastern Mediterranean. Accumulated knowledge on lionfish invasions in the western Atlantic Ocean has shown that it is a successful invader and can have negative impacts on native species, indirect ecological repercussions and economic effects on local human societies. Here we analysed genetic sequences of lionfish from Cyprus as well as data from the whole distribution of the species, targeting the mtDNA markers cytochrome c oxidase subunit 1 (COI) and the control region (CR). Our results reflect a pattern of repeated introductions into the Mediterranean from the northern Red Sea and a secondary spread of this species west to Rhodes and Sicily. Presented results agree with previously published studies highlighting the genetic similarity with individuals from the northern Red Sea. Nevertheless, some individuals from Cyprus, in addition to those coming via the Suez Canal, were genetically similar to fish from the Indian Ocean, indicating genetic homogeneity among populations of P. miles across its current distribution, possibly facilitated by the ornamental fish trade and/or transport through ballast water. Full article
(This article belongs to the Special Issue Biological Invasions 2020 Horizon)
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Open AccessArticle
Local-Scale Bat Guild Activity Differs with Rice Growth Stage at Ground Level in the Philippines
Diversity 2019, 11(9), 148; https://doi.org/10.3390/d11090148 - 27 Aug 2019
Viewed by 494
Abstract
High-flying insectivorous bats, as wide-ranging generalist insectivores, are valuable consumers of high-altitude migrating pests of rice in Southeast Asia. Here, we documented the behavior of relatively low-flying bats over irrigated rice to elucidate their potential role as predators of rice-associated pest insects in [...] Read more.
High-flying insectivorous bats, as wide-ranging generalist insectivores, are valuable consumers of high-altitude migrating pests of rice in Southeast Asia. Here, we documented the behavior of relatively low-flying bats over irrigated rice to elucidate their potential role as predators of rice-associated pest insects in the Philippines. Specifically, we tested the local-scale effects of rice stage, particularly seedling and late vegetative stages, and time of night on acoustic activity of bats foraging near ground level within three functional guilds (based on foraging distance from background clutter). We also monitored bat activity from two 50 m-high towers to assess the vertical extent of relatively low-flying guilds, as well as document high-flying bat guild presence and temporal behavior. At ground level, the most active guild biased their activity and feeding over early growth stage fields, but also foraged at tower level. Activity of the bat guild adept at foraging closest to vegetation did not vary with time of night or rice stage and was absent from tower recordings. High-flying bats were predictably rare at rice level, but exhibited high foraging intensity at 50 m. Given the well-documented, sequential arrival of insect guilds with growth stage, these data suggest that at ground level edge-space bats may be important consumers of detritivores (e.g., mosquitoes). Moreover, our data suggest that just as habitat heterogeneity enhances the services of arthropod predators, these management practices also enhance bat activity and, presumably, their contribution to pest suppression. Full article
(This article belongs to the Section Animal Diversity)
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Open AccessArticle
Ecological and Conservation Correlates of Rarity in New World Pitvipers
Diversity 2019, 11(9), 147; https://doi.org/10.3390/d11090147 - 27 Aug 2019
Viewed by 774
Abstract
Rare species tend to be especially sensitive to habitat disturbance, making them important conservation targets. Thus, rarity patterns might be an important guide to conservation efforts. Rabinowitz’s approach defines rarity using a combination of geographical range, habitat specificity, and local abundance, and is [...] Read more.
Rare species tend to be especially sensitive to habitat disturbance, making them important conservation targets. Thus, rarity patterns might be an important guide to conservation efforts. Rabinowitz’s approach defines rarity using a combination of geographical range, habitat specificity, and local abundance, and is frequently used in conservation prioritization. Herein, we use Rabinowitz’s approach to classify the New World (NW) pitvipers (family Viperidae) regarding rarity. We tested whether body size and latitude could predict rarity, and we compared rarity patterns with extinction risk assessments and other prioritization methods in order to detect rare species not classified as threatened or prioritized. Most NW pitvipers have large geographical ranges, high local abundances, and narrow habitat breadths. There are 11.8% of NW pitviper species in the rarest category and they occur along the Pacific coast of Mexico, in southern Central America, in the Andean region of Ecuador, and in eastern Brazil. Rarity in NW pitvipers is inversely related to latitude but is not related to body size. Our results indicate that additional species of NW pitvipers are threatened and/or should be prioritized for conservation. Combining complementary approaches to detect rare and threatened species may substantially improve our knowledge on the conservation needs of NW pitvipers. Full article
(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)
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Open AccessArticle
An Alien Invader is the Cause of Homogenization in the Recipient Ecosystem: A Simulation-Like Approach
Diversity 2019, 11(9), 146; https://doi.org/10.3390/d11090146 - 26 Aug 2019
Viewed by 385
Abstract
Biotic homogenization is an expected effect of biological invasions. Invasive alien species typically show great adaptability to a wide range of environmental conditions and may expand into different habitats, thus reducing the dissimilarity among the recipient communities. We tested this assumption by analyzing [...] Read more.
Biotic homogenization is an expected effect of biological invasions. Invasive alien species typically show great adaptability to a wide range of environmental conditions and may expand into different habitats, thus reducing the dissimilarity among the recipient communities. We tested this assumption by analyzing a comprehensive database (78 species × 229 samples) collected between 2012 and 2017 in the marine protected area of Portofino (NW Italy), where Caulerpa cylindracea, one of the worst invaders in the Mediterranean Sea, exhibits high substratum cover at depths between 1 m and 45 m in 14 different communities (identified according to the European Nature Information System EUNIS for habitat classification). Five samples for each of the eight depth zones (i.e., 5 m, 10 m, 15 m, 20 m, 25 m, 30 m, 35 m, and 40 m) were randomly re-sampled from the comprehensive database to produce a dataset of 67 species × 40 samples. Then, a second dataset of 66 species × 40 samples was simulated by excluding Caulerpa cylindracea. Both re-sampled datasets underwent multivariate analysis. In the presence of C. cylindracea, the overall similarity among samples was higher, thus indicating homogenization of the rocky reef communities of Portofino Marine Protected Area. Continued monitoring activity is needed to understand and assess the pattern and extent of C. cylindracea’s inclusion in the recipient ecosystems. Full article
(This article belongs to the Special Issue Biological Invasions 2020 Horizon)
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Open AccessArticle
A New Species of Terrestrial-Breeding Frog (Amphibia, Strabomantidae, Noblella) from the Upper Madre De Dios Watershed, Amazonian Andes and Lowlands of Southern Peru
Diversity 2019, 11(9), 145; https://doi.org/10.3390/d11090145 - 26 Aug 2019
Viewed by 687
Abstract
We describe and name a new species of Noblella Barbour, 1930 (Strabomantidae) from southern Peru. Key diagnostic characteristics of the new species include the presence of a short, oblique fold-like tubercle on the ventral part of the tarsal region, two phalanges on finger [...] Read more.
We describe and name a new species of Noblella Barbour, 1930 (Strabomantidae) from southern Peru. Key diagnostic characteristics of the new species include the presence of a short, oblique fold-like tubercle on the ventral part of the tarsal region, two phalanges on finger IV, and an evident tympanum. The elevational distribution of the new species spans 1250 m (240–1490 m) from lowland Amazon rainforest to montane forest on the eastern slopes of the Andes. Full article
(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)
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Open AccessArticle
A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)
Diversity 2019, 11(9), 144; https://doi.org/10.3390/d11090144 - 23 Aug 2019
Cited by 1 | Viewed by 589
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting [...] Read more.
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species. Full article
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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