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Diversity, Volume 11, Issue 7 (July 2019)

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Cover Story (view full-size image) Systematics in the phylogenomic era utilizes high-throughput sequencing to estimate phylogenies [...] Read more.
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Open AccessArticle
An Introduction to the Study of Gastrotricha, with a Taxonomic Key to Families and Genera of the Group
Diversity 2019, 11(7), 117; https://doi.org/10.3390/d11070117
Received: 27 June 2019 / Revised: 16 July 2019 / Accepted: 17 July 2019 / Published: 23 July 2019
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Abstract
Gastrotricha is a group of meiofaunal-sized, free-living invertebrates present in all aquatic ecosystems. The phylum includes over 860 species globally, of which 505 nominal species have been recorded in marine sandy sediments; another 355 taxa inhabit the freshwater environments, where they are recurrent [...] Read more.
Gastrotricha is a group of meiofaunal-sized, free-living invertebrates present in all aquatic ecosystems. The phylum includes over 860 species globally, of which 505 nominal species have been recorded in marine sandy sediments; another 355 taxa inhabit the freshwater environments, where they are recurrent members of the periphyton and epibenthos, and, to a lesser degree, of the plankton and interstitial fauna. Gastrotrichs are part of the permanent meiofauna and, in general, they rank among the top five groups for abundance within meiobenthic assemblages. The diversity, abundance, and ubiquity of Gastrotricha allow us to suppose an important role for these animals in aquatic ecosystems; however, ecological studies to prove this idea have been comparatively very few. This is mainly because the small size and transparency of their bodies make gastrotrichs difficult to discover in benthic samples; moreover, their contractility and fragility make their handling and morphological survey of the specimens rather difficult. Here we offer an overview, describe the basic techniques used to study these animals, and provide a key to known genera in an attempt to promote easy identification and to increase the number of researchers who may be interested in conducting studies on this understudied ecological group of microscopic organisms. Full article
(This article belongs to the Special Issue Meiofauna Biodiversity and Ecology)
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Open AccessArticle
Accuracy and Precision of Low-Cost Echosounder and Automated Data Processing Software for Habitat Mapping in a Large River
Diversity 2019, 11(7), 116; https://doi.org/10.3390/d11070116
Received: 30 June 2019 / Revised: 12 July 2019 / Accepted: 17 July 2019 / Published: 19 July 2019
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Abstract
The development of consumer hydroacoustic systems continues to advance, enabling the use of low-cost methods for professional mapping purposes. Information describing habitat characteristics produced with a combination of low-cost commercial echosounder (Lowrance HDS) and a cloud-based automated data processing tool (BioBase EcoSound) was [...] Read more.
The development of consumer hydroacoustic systems continues to advance, enabling the use of low-cost methods for professional mapping purposes. Information describing habitat characteristics produced with a combination of low-cost commercial echosounder (Lowrance HDS) and a cloud-based automated data processing tool (BioBase EcoSound) was tested. The combination frequently underestimated water depth, with a mean absolute error of 0.17 ± 0.13 m (avg ± 1SD). The average EcoSound bottom hardness value was high (0.37–0.5) for all the substrate types found in the study area and could not be used to differentiate between the substrate size classes that varied from silt to bedrock. Overall, the bottom hardness value is not informative in an alluvial river bed setting where the majority of the substrate is composed of hard sands, gravels, and stones. EcoSound separated vegetation presence/absence with 85–100% accuracy and assigned vegetation height (EcoSound biovolume) correctly in 55% of instances but often overestimated it in other instances. It was most accurate when the vegetation canopy was ≤25% or >75% of the water column. Overall, as a low-cost, easy-to-use application EcoSound offers rapid data collection and allows users with no specialized skill requirements to make more detailed bathymetry and vegetation maps than those typically available for many rivers, lakes, and estuaries. Full article
(This article belongs to the Special Issue Aquatic Environmental Monitoring and Assessment)
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Open AccessReview
Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
Diversity 2019, 11(7), 115; https://doi.org/10.3390/d11070115
Received: 8 June 2019 / Revised: 7 July 2019 / Accepted: 15 July 2019 / Published: 18 July 2019
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Abstract
Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts [...] Read more.
Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up. Full article
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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Open AccessArticle
Species Diversity of Epilithon Diatoms and the Quality of the Waters of the Donuzlav Gulf Ecosystem (Crimea, the Black Sea)
Diversity 2019, 11(7), 114; https://doi.org/10.3390/d11070114
Received: 13 June 2019 / Revised: 4 July 2019 / Accepted: 10 July 2019 / Published: 18 July 2019
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Abstract
In this work, the species diversity of epilithon diatoms of Donuzlav Gulf (Crimean coastal waters of the Black Sea) is presented for the first time. A total of 60 taxa of Bacillariophyta belonging to 3 classes, 18 families and 34 genera were found. [...] Read more.
In this work, the species diversity of epilithon diatoms of Donuzlav Gulf (Crimean coastal waters of the Black Sea) is presented for the first time. A total of 60 taxa of Bacillariophyta belonging to 3 classes, 18 families and 34 genera were found. The largest number of species (45) of diatoms was observed in summer, and the smallest number of species (12) in winter. A total of 25 saprobity indicator species of diatoms was found on the epilithon, 12 taxa of which belong to a group of betamesosaprobionts—indicators of moderate organic pollution of water. Marine species comprise 55% and brackish-marine ones make up 37% of them, but no freshwater species were identified. The diatom community was dominated by cosmopolites (32%) and arctic–boreal–tropical species (27%). The maximal abundance (186.2 × 103 cells cm−2) and biomass (0.083 mg cm−2) of diatoms was noted in June 2018 at salinity 16.58‰ and T = 24.4 °C with the dominant cosmopolites species of Licmophora abbreviata and Cocconeis scutellum. The minimum values, 14.8 × 103 cells cm−2 and 0.005 mg cm−2, were observed in January 2019 at salinity 16.86‰ and T = 9.0 °C with the dominant Berkeleya rutilans and Nitzschia hybrida f. hyalina. The high values of BOD5, oxidizability, silicon, Norg and Porg were noted, indicating a certain degree of water pollution by domestic sewage. It has been shown that the pollution in the southwestern part of the Donuzlav Gulf is greatest since this part of the coast was populated most densely in comparison with the northern coast of the Gulf where there are no coastal settlements except for two mariculture farms. Full article
(This article belongs to the Special Issue Freshwater Algal Diversity and Bio-Indication of Water Resources)
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Open AccessReview
Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins
Diversity 2019, 11(7), 113; https://doi.org/10.3390/d11070113
Received: 13 May 2019 / Revised: 28 June 2019 / Accepted: 12 July 2019 / Published: 16 July 2019
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Abstract
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively [...] Read more.
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential. Full article
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Open AccessArticle
Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.
Diversity 2019, 11(7), 112; https://doi.org/10.3390/d11070112
Received: 18 May 2019 / Revised: 30 June 2019 / Accepted: 1 July 2019 / Published: 15 July 2019
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Abstract
Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, [...] Read more.
Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present. Full article
(This article belongs to the Section Microbial Diversity)
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Open AccessArticle
Seasonal Physiological Parameters and Phytotelmata Bacterial Diversity of Two Bromeliad Species (Aechmea gamosepala and Vriesea platynema) from the Atlantic Forest of Southern Brazil
Diversity 2019, 11(7), 111; https://doi.org/10.3390/d11070111
Received: 13 May 2019 / Revised: 1 June 2019 / Accepted: 3 June 2019 / Published: 14 July 2019
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Abstract
The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea [...] Read more.
The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at an Atlantic Forest site and used 16S rDNA metabarcoding to survey the microbial communities inhabiting their tanks. We observed that levels of some nutrients (e.g., nitrogen) varied across seasons consistently in both species, while others (e.g., phenolic compounds) presented considerable differences between the two bromeliads. In contrast, patterns of tank microbial diversity did not follow a similar temporal trend. There was extensive variation in microbial composition among samples, which included intra-specific differences but also some consistent differences between the two bromeliads. For example, Citrobacter, Klebsiella and Pantoea presented significantly different abundances in the two species. Interestingly, the dominant bacterial genera in both species included Pseudomonas and Enterobacter, which have been reported to include plant-beneficial species. Overall, our data contribute to the characterization of the nutritional status of Atlantic Forest bromeliads and the composition of their prokaryotic communities, laying the foundation for detailed investigations targeting the ecological interactions between these plants and their associated microbes. Full article
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Open AccessArticle
How Roads Affect the Spatial Use of the Guanaco in a South American Protected Area: Human Connectivity vs Animal Welfare
Diversity 2019, 11(7), 110; https://doi.org/10.3390/d11070110
Received: 19 March 2019 / Revised: 24 June 2019 / Accepted: 2 July 2019 / Published: 12 July 2019
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Abstract
Roads can affect animals as well as their habits at different levels. Avoidance behavior is a common response of animals to this type of perturbation, preventing access to areas rich in resources. The effects of roads on ungulates have not been studied in [...] Read more.
Roads can affect animals as well as their habits at different levels. Avoidance behavior is a common response of animals to this type of perturbation, preventing access to areas rich in resources. The effects of roads on ungulates have not been studied in South America extensively, especially in arid environments. We have studied the space use by ungulates in relation to roads, using a dung heap count and camera traps. The aim was to evaluate whether paved road and unpaved road may have an effect on the spatial use of a low density population of guanacos (Lama guanicoe) in Ischigualasto Provincial Park, Argentina. We observed an increase in dung heap abundance in unpaved road as respect to paved road, this difference was larger for both. Besides, we recorded less individuals in paved road zones than in unpaved road zones. This showed that roads, especially paved roads, negatively affect the space used by guanacos. Our results are relevant to the management and conservation of animal populations in protected areas since spatial segregation due to the presence of roads may lead to the isolation of individuals. It is important to pay attention and further assess the effects that roads can have in the native fauna. Full article
(This article belongs to the Special Issue Impacts of Linear Infrastructures on Wildlife)
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Open AccessArticle
A Phylogenomic Supertree of Birds
Diversity 2019, 11(7), 109; https://doi.org/10.3390/d11070109
Received: 31 May 2019 / Revised: 5 July 2019 / Accepted: 7 July 2019 / Published: 10 July 2019
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Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in [...] Read more.
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well. Full article
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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Open AccessArticle
Phylogenetic Signal of Indels and the Neoavian Radiation
Diversity 2019, 11(7), 108; https://doi.org/10.3390/d11070108
Received: 3 June 2019 / Revised: 3 July 2019 / Accepted: 4 July 2019 / Published: 6 July 2019
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Abstract
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 [...] Read more.
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves. Full article
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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Open AccessArticle
A Vulnerability Analysis of Coral Reefs in Coastal Ecotourism Areas for Conservation Management
Diversity 2019, 11(7), 107; https://doi.org/10.3390/d11070107
Received: 10 May 2019 / Revised: 27 June 2019 / Accepted: 1 July 2019 / Published: 6 July 2019
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Abstract
Coral reef ecosystems provide many ecological, economic, and social benefits. Despite their numerous functions, coral reefs are in a vulnerable state due to the effects of human activities. The condition of coral reefs has decreased in many parts of the world. Therefore, coral [...] Read more.
Coral reef ecosystems provide many ecological, economic, and social benefits. Despite their numerous functions, coral reefs are in a vulnerable state due to the effects of human activities. The condition of coral reefs has decreased in many parts of the world. Therefore, coral reef examinations need to be carried out continuously in order to formulate management strategies that can reduce their vulnerability over time. This study aims to analyze the vulnerability index of coral reefs, the sensitivity of coral reefs to the causes of vulnerability, and the adaptive capacity to anticipate vulnerability. The primary data are the perceptions of respondents’ who filled out a prepared questionnaire which included eight dimensions: information on the environmental conditions, fishing ports, fishing areas, coastline settlements, tourism management, tourism attractions, socio-economic conditions and population, and aquaculture. The data were analyzed using multidimensional scaling (MDS). The results of the analysis revealed that fishing ports, fishing areas, and environmental condition are high vulnerability indexes which cause damage to coral reefs. The highest coral reef vulnerability sensitivity was found to be triggered by the distance from fishing areas and the distance from fishing vessel channels. An inverse relationship between vulnerability and adaptive capacity was shown. Hence distance from fishing areas and distance from fishing vessel channels are the attributes that have low adaptive capacity. Full article
(This article belongs to the Section Marine Diversity)
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Open AccessArticle
The Prevalence of Single-Specimen/Locality Species in Insect Taxonomy: An Empirical Analysis
Diversity 2019, 11(7), 106; https://doi.org/10.3390/d11070106
Received: 18 June 2019 / Revised: 3 July 2019 / Accepted: 4 July 2019 / Published: 6 July 2019
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Abstract
Although about two million species have been named, our knowledge about the biodiversity of many taxonomic groups remains inadequate and incomplete. There has been increased taxonomic effort for the discovery of more species and their geographical distribution information. During this process, species collected [...] Read more.
Although about two million species have been named, our knowledge about the biodiversity of many taxonomic groups remains inadequate and incomplete. There has been increased taxonomic effort for the discovery of more species and their geographical distribution information. During this process, species collected only from a single specimen/locality often appear. However, there are very few empirical data available to understand the current situation of single specimen/locality species in insect taxonomy. In this paper, we collected 1261 articles containing 4811 insect species from ZooKeys between 2009 and 2017, and we extracted data, including the publication date, number of specimens/locality, and DNA usage. Our analyses demonstrated that 21.53% and 21.74% of new species were described from only one specimen and one locality, respectively, and approximately half of all new species were published based on fewer than five specimens. Meanwhile, the rate of single-specimen species in papers with or without DNA data was 15.06% and 23.43%, respectively, which indicates that incorporating DNA data in species descriptions might effectively decrease the occurrence of single-specimen species. We suggest that taxonomists should adopt more beneficial practices, such as increasing specimen diversity, incorporating DNA data, and improving international collaboration, in the description of new species. Full article
(This article belongs to the Special Issue Biodiversity of Insect)
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Open AccessArticle
Community Structures of Bacteria, Archaea, and Eukaryotic Microbes in the Freshwater Glacier Lake Yukidori-Ike in Langhovde, East Antarctica
Diversity 2019, 11(7), 105; https://doi.org/10.3390/d11070105
Received: 3 June 2019 / Revised: 2 July 2019 / Accepted: 4 July 2019 / Published: 6 July 2019
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Abstract
Since most studies about community structures of microorganisms in Antarctic terrestrial lakes using molecular biological tools are mainly focused on bacteria, limited information is available about archaeal and eukaryotic microbial diversity. In this study, the biodiversity of microorganisms belonging to all three domains [...] Read more.
Since most studies about community structures of microorganisms in Antarctic terrestrial lakes using molecular biological tools are mainly focused on bacteria, limited information is available about archaeal and eukaryotic microbial diversity. In this study, the biodiversity of microorganisms belonging to all three domains in a typical Antarctic freshwater glacier lake (Yukidori-Ike) was revealed using small subunit ribosomal RNA (SSU rRNA) clone library analysis. The bacterial clones were grouped into 102 operational taxonomic units (OTUs) and showed significant biodiversity. Betaproteobacteria were most frequently detected, followed by Cyanobacteria, Bacteroidetes, and Firmicutes as major lineages. In contrast to the bacterial diversity, much lower archaeal diversity, consisting of only two OTUs of methanogens, was observed. In the eukaryotic microbial community consisting of 20 OTUs, Tardigradal DNA was remarkably frequently detected. Genera affiliated with the phyla Ciliophora, Cryptomycota, Chlorophyta, Bacillariophyta, and Apusozoa were also detected. The biodiversity and species compositions of the whole microbial community of Lake Yukidori-Ike are similar to those of freshwater environments in temperate regions but are different from saline lakes in Antarctica, indicating that the salinity seems to affect the microbial composition more than the temperature. Full article
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Open AccessArticle
An Anomalous Phylogenetic Position for Deraiotrema platacis Machida, 1982 (Lepocreadiidae) from Platax pinnatus on the Great Barrier Reef
Diversity 2019, 11(7), 104; https://doi.org/10.3390/d11070104
Received: 16 May 2019 / Revised: 11 June 2019 / Accepted: 15 June 2019 / Published: 4 July 2019
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Abstract
The monotypic genus Deraiotrema Machida, 1982 has only been reported once, from the orbicular batfish Platax orbicularis (Forsskål) in the waters around Palau in Micronesia (Machida, 1982). It has a body-shape similar to other lepocreadiids from batfishes, such as species of Bianium Stunkard, [...] Read more.
The monotypic genus Deraiotrema Machida, 1982 has only been reported once, from the orbicular batfish Platax orbicularis (Forsskål) in the waters around Palau in Micronesia (Machida, 1982). It has a body-shape similar to other lepocreadiids from batfishes, such as species of Bianium Stunkard, 1930 and Diploproctodaeum La Rue, 1926, but differs in having multiple testes in ventral and dorsal layers. Here we report Deraiotrema platacis Machida, 1982 for just the second time, infecting the dusky batfish Platax pinnatus (Linnaeus) from the waters off Lizard Island on the northern Great Barrier Reef. We present a molecular phylogenetic analysis of the position of this genus inferred from 28S rDNA sequences. Surprisingly, we find the species most closely related to Echeneidocoelium indicum despite the infection of completely unrelated hosts and the presence of two characters (lateral fold in the forebody and multiple testes) that are found elsewhere in the Lepocreadiidae. We conclude that homoplasy within the Lepocreadiidae is extensive and that morphology-based prediction of relationships has little prospect of success. Full article
(This article belongs to the Special Issue Taxonomy and Diversity of Aquaculture and Fisheries Parasites)
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Open AccessArticle
Microbial Community in Hyperalkaline Steel Slag-Fill Emulates Serpentinizing Springs
Diversity 2019, 11(7), 103; https://doi.org/10.3390/d11070103
Received: 21 May 2019 / Revised: 17 June 2019 / Accepted: 21 June 2019 / Published: 30 June 2019
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Abstract
To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions offer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. [...] Read more.
To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions offer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. Yet hyperalkaline freshwater systems also occur both naturally and anthropogenically, such as the slag fill aquifers around former Lake Calumet (Chicago, IL, USA). In this study, 16S rRNA gene sequences and metagenomic sequence libraries were collected to assess the taxonomic composition and functional potential of microbes present in these slag-polluted waterways. Relative 16S rRNA gene abundances in Calumet sediment and water samples describe community compositions not significantly divergent from those in nearby circumneutral conditions. Major differences in composition are mainly driven by Proteobacteria, primarily one sequence cluster closely related to Hydrogenophaga, which comprises up to 85% of 16S rRNA gene abundance in hyperalkaline surface sediments. Sequence identity indicates this novel species belongs to the recently established genus Serpentinomonas, a bacterial lineage associated with natural freshwater hyperalkaline serpentinizing springs. Full article
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Open AccessArticle
New Material of Paleocene-Eocene Pellornis (Aves: Gruiformes) Clarifies the Pattern and Timing of the Extant Gruiform Radiation
Diversity 2019, 11(7), 102; https://doi.org/10.3390/d11070102
Received: 10 May 2019 / Revised: 25 June 2019 / Accepted: 26 June 2019 / Published: 28 June 2019
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Abstract
Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered [...] Read more.
Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered to comprise a partial postcranial skeleton. However, additional mechanical preparation of the nodule containing the holotype revealed that the skeleton is nearly complete and includes a well-preserved skull. In addition to extracting new information from the holotype, we identify and describe two additional specimens of P. mikkelseni which reveal further morphological details of the skeleton. Together, these specimens show that P. mikkelseni possessed a schizorhinal skull and shared many features with the well-known Paleogene Messelornithidae (“Messel rails”). To reassess the phylogenetic position of P. mikkelseni, we modified an existing morphological dataset by adding 20 characters, four extant gruiform taxa, six extinct gruiform taxa, and novel scorings based on the holotype and referred specimens. Phylogenetic analyses recover a clade containing P. mikkelseni, Messelornis, Songzia and crown Ralloidea, supporting P. mikkelseni as a crown gruiform. The phylogenetic position of P. mikkelseni illustrates that some recent divergence time analyses have underestimated the age of crown Gruiformes. Our results suggest a Paleocene origin for this important clade, bolstering evidence for a rapid early radiation of Neoaves following the end-Cretaceous mass extinction. Full article
(This article belongs to the Special Issue Origins of Modern Avian Biodiversity)
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Open AccessArticle
Visual Head Counts: A Promising Method for Efficient Monitoring of Diamondback Terrapins
Diversity 2019, 11(7), 101; https://doi.org/10.3390/d11070101
Received: 3 April 2019 / Revised: 22 June 2019 / Accepted: 24 June 2019 / Published: 27 June 2019
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Abstract
Determining the population status of the diamondback terrapin (Malaclemys terrapin spp.) is challenging due to their ecology and limitations associated with traditional sampling methods. Visual counting of emergent heads offers a promising, efficient, and non-invasive method for generating abundance estimates of terrapin [...] Read more.
Determining the population status of the diamondback terrapin (Malaclemys terrapin spp.) is challenging due to their ecology and limitations associated with traditional sampling methods. Visual counting of emergent heads offers a promising, efficient, and non-invasive method for generating abundance estimates of terrapin populations across broader spatial scales than has been achieved using capture–recapture, and can be used to quantify determinants of spatial variation in abundance. We conducted repeated visual head count surveys along the shoreline of Wellfleet Bay in Wellfleet, Massachusetts, and analyzed the count data using a hierarchical modeling framework designed specifically for repeated count data: the N-mixture model. This approach allows for simultaneous modeling of imperfect detection to generate estimates of true terrapin abundance. Detection probability was lowest when temperatures were coldest and when wind speed was highest. Local abundance was on average higher in sheltered sites compared to exposed sites and declined over the course of the sampling season. We demonstrate the utility of pairing visual head counts and N-mixture models as an efficient method for estimating terrapin abundance and show how the approach can be used to identifying environmental factors that influence detectability and distribution. Full article
(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)
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Open AccessArticle
A Comparison of the Population Genetic Structure and Diversity between a Common (Chrysemys p. picta) and an Endangered (Clemmys guttata) Freshwater Turtle
Diversity 2019, 11(7), 99; https://doi.org/10.3390/d11070099
Received: 13 March 2019 / Revised: 18 June 2019 / Accepted: 19 June 2019 / Published: 26 June 2019
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Abstract
The northeastern United States has experienced dramatic alteration to its landscape since the time of European settlement. This alteration has had major impacts on the distribution and abundance of wildlife populations, but the legacy of this landscape change remains largely unexplored for most [...] Read more.
The northeastern United States has experienced dramatic alteration to its landscape since the time of European settlement. This alteration has had major impacts on the distribution and abundance of wildlife populations, but the legacy of this landscape change remains largely unexplored for most species of freshwater turtles. We used microsatellite markers to characterize and compare the population genetic structure and diversity between an abundant generalist, the eastern painted turtle (Chrysemys p. picta), and the rare, more specialized, spotted turtle (Clemmys guttata) in Rhode Island, USA. We predicted that because spotted turtles have disproportionately experienced the detrimental effects of habitat loss and fragmentation associated with landscape change, that these effects would manifest in the form of higher inbreeding, less diversity, and greater population genetic structure compared to eastern painted turtles. As expected, eastern painted turtles exhibited little population genetic structure, showed no evidence of inbreeding, and little differentiation among sampling sites. For spotted turtles, however, results were consistent with certain predictions and inconsistent with others. We found evidence of modest inbreeding, as well as tentative evidence of recent population declines. However, genetic diversity and differentiation among sites were comparable between species. As our results do not suggest any major signals of genetic degradation in spotted turtles, the southern region of Rhode Island may serve as a regional conservation reserve network, where the maintenance of population viability and connectivity should be prioritized. Full article
(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)
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Open AccessArticle
Spatial Response to Linear Infrastructures by the Endangered Golden Lion Tamarin
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Diversity 2019, 11(7), 100; https://doi.org/10.3390/d11070100
Received: 13 April 2019 / Revised: 3 June 2019 / Accepted: 6 June 2019 / Published: 26 June 2019
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Abstract
Linear infrastructures are a primary driver of economic development. However, they also can negatively affect wildlife by mortality and the barrier effect. In this paper, we address how paved and unpaved roads, high-tension power lines, and gas/oil pipelines affect home range size, core [...] Read more.
Linear infrastructures are a primary driver of economic development. However, they also can negatively affect wildlife by mortality and the barrier effect. In this paper, we address how paved and unpaved roads, high-tension power lines, and gas/oil pipelines affect home range size, core areas, and movement in an endangered primate, the golden lion tamarin (GLT). Location data were recorded using radio telemetry on 16 groups in two protected areas and in privately owned forest fragments. The GLT’s home range, not core area, increased in size for the groups that occupied locations far from linear infrastructures; home range was also significantly influenced by available forest size. None of the home ranges contained a road, but home ranges did contain power lines. GLTs used the surrounding landscape near all types of infrastructure. Movement analysis showed that most of the step lengths (distances between subsequent locations) were less than 100 m between two consecutive locations, but step length was longer for roads and longer for groups in fully forested habitats. Tamarins avoided paved roads when in close proximity to this type of infrastructure; this behavior increased in areas without adequate adjacent forest habitat. Our results show that linear infrastructures differ in their level of impact: roads can act as a barrier, whereas other types of infrastructure have minimal effect on movement and home range. We discuss these differences in impact in terms of structure, maintenance schedules, and edge effects of infrastructure. Full article
(This article belongs to the Special Issue Impacts of Linear Infrastructures on Wildlife)
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