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Diversity, Volume 10, Issue 2 (June 2018)

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Editorial

Jump to: Research, Review

Open AccessEditorial Special Issue: Plant Genetics and Biotechnology in Biodiversity
Diversity 2018, 10(2), 19; https://doi.org/10.3390/d10020019
Received: 21 March 2018 / Revised: 21 March 2018 / Accepted: 23 March 2018 / Published: 27 March 2018
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Abstract
The rapid progress and increasing affordability of novel investigation tools in plant genetics and biotechnology offer previously inaccessible opportunities for the exploitation of plant genetic diversity in agriculture. The Special Issue was lunched to highlight how new technologies are improving both genotyping and
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The rapid progress and increasing affordability of novel investigation tools in plant genetics and biotechnology offer previously inaccessible opportunities for the exploitation of plant genetic diversity in agriculture. The Special Issue was lunched to highlight how new technologies are improving both genotyping and phenotyping methods, thus allowing us to uncover crop diversity and use genetic variability for plant breeding with remarkable precision and speed. Three thematic reviews report on scientific, technological, and legal advances in plant diversity and agriculture. Three contributions provide specific examples of the exploitation of different kinds of genetic resources, ranging from landraces to mutant populations. Six research articles are illustrative examples of the study of molecular and/or phenotypic diversity to address basic or applied questions in different plant species. Finally, this SI was also launched to honor the memory of Prof. Gian Tommaso Scarascia Mugnozza and a dedicated Editorial acknowledges his work in plant breeding and biodiversity protection. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)

Research

Jump to: Editorial, Review

Open AccessArticle Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors
Diversity 2018, 10(2), 17; https://doi.org/10.3390/d10020017
Received: 5 February 2018 / Revised: 8 March 2018 / Accepted: 15 March 2018 / Published: 21 March 2018
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Abstract
The genus Eragrostis consists of 350 species, including tef (Eragrostis tef (Zucc.) Trotter), the only cultivated species in this genus. Very little is known about the genetic potential of these species for tef improvement and genomics research. Here, we investigated a germplasm
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The genus Eragrostis consists of 350 species, including tef (Eragrostis tef (Zucc.) Trotter), the only cultivated species in this genus. Very little is known about the genetic potential of these species for tef improvement and genomics research. Here, we investigated a germplasm panel consisting of 40 Eragrostis species and 42 tef lines with single nucleotide polymorphism (SNP) data generated using the genotyping by sequencing (GBS) protocol. Thousands of SNPs were identified genome-wide from the germplasm panel. High-quality SNPs were used to assess sequence similarity and/or divergence, genetic diversity, population structure, and phylogenetic relationships. Mapping individual reads to the tef reference genome revealed that of the 40 wild Eragrostis species included in this study, E. pilosa, E. aethiopica, E. obtusa, E. ferruginea, E. lugens, and E. lehmanniana had 92% of their sequences represented in the tef reference genome. In the maximum likelihood phylogenetic analysis, these wild species clearly showed grouping in the clade consisting of the entire tef germplasm. Population structure analysis showed two major clusters consistent with the germplasm class information and the inferred phylogenetic relationships. The wild Eragrostis species were more diverse than the tef cultivars and could therefore potentially be used to enrich the tef gene pool. The SNP dataset and the results documented here are taxonomically the most inclusive to date and could be a useful informational tool for the design of genomics-informed tef breeding and research. Full article
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Open AccessArticle Significance of Mangrove Biodiversity Conservation in Fishery Production and Living Conditions of Coastal Communities in Sri Lanka
Diversity 2018, 10(2), 20; https://doi.org/10.3390/d10020020
Received: 8 February 2018 / Revised: 22 March 2018 / Accepted: 27 March 2018 / Published: 30 March 2018
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Abstract
Sri Lanka is an island nation where ~59% of the population live in coastal regions. The main income source in these areas is fishing, which contributes to ~44% of the national GDP. Fishery resources depend on mangroves, especially in estuaries and lagoons, as
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Sri Lanka is an island nation where ~59% of the population live in coastal regions. The main income source in these areas is fishing, which contributes to ~44% of the national GDP. Fishery resources depend on mangroves, especially in estuaries and lagoons, as mangroves provide the best nursery grounds for both brackish and marine species that are significant for the island’s fishing industry. However, growing pressures from an increasing population and development are causing substantial damage to mangroves resulting in loss of mangrove diversity. We analyzed whether variation in mangrove diversity within a lagoon system affects fishery production and livelihoods. Along the lagoon we selected three sites, which were 5 km apart from each other, for the survey. We used three 50 m long transects at each site for faunal and floral diversity assessments. The fishery catch was recorded from three crafts in each side. The socio-economic survey was conducted in 30 households per site using a standard questionnaire. In the site with the highest floral and faunal diversity, we also recorded the highest fish catch, but not the highest crab or shrimp catches. Our results confirm that higher mangrove diversity—and not just area—supports higher income generation. Thus, future development should prioritize biodiversity conservation in coastal regions. Full article
(This article belongs to the Special Issue Mangrove Ecology and Conservation)
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Open AccessArticle Statistical Evaluation of Monophyly in the ‘Broad-Nosed Weevils’ through Molecular Phylogenetic Analysis Combining Mitochondrial Genome and Single-Locus Sequences (Curculionidae: Entiminae, Cyclominae, and Hyperinae)
Diversity 2018, 10(2), 21; https://doi.org/10.3390/d10020021
Received: 20 January 2018 / Revised: 22 March 2018 / Accepted: 2 April 2018 / Published: 6 April 2018
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Abstract
Establishing well-supported monophyletic groups is a key requirement for producing a natural classification that reflects evolutionary descent. In a phylogenetic framework this is best achieved through dense taxon sampling and the analysis of a robust character dataset, combined with statistical testing of topological
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Establishing well-supported monophyletic groups is a key requirement for producing a natural classification that reflects evolutionary descent. In a phylogenetic framework this is best achieved through dense taxon sampling and the analysis of a robust character dataset, combined with statistical testing of topological hypotheses. This study assesses the monophyly of tribes and subfamilies within the diverse ‘broad-nosed weevils’ (Curculionidae: Entiminae, Cyclominae and Hyperinae) through analysis of single-locus sequence data for mitochondrial cox1 and rrnL genes, in combination with a ‘backbone’ of complete and near-complete mitochondrial genome sequences. Maximum likelihood phylogenetic analyses incorporating topological constraints for various higher-taxa were statistically tested using the AU, SH, and KH tests, which indicated that three tribes within Entiminae, as presently classified, are not monophyletic. Moderate and high bootstrap support was also consistent with two entimine tribes (Peritelini and Cylydrorhinini) being each recovered as monophyletic in an unconstrained analysis. Furthermore, one genus of cyclomine weevils (Aphela) is recovered outside the clade of ‘broad-nosed weevils’, although its taxonomic placement remains uncertain. It is apparent that the present approach may be hampered by limited taxon sampling in the ‘backbone’ dataset, rendering it difficult for divergent taxa to robustly match to their closest lineages. However, with improved taxon sampling of the mitogenome tree, the general approach can be a useful taxonomic tool for weevils. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessArticle Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia
Diversity 2018, 10(2), 22; https://doi.org/10.3390/d10020022
Received: 15 March 2018 / Revised: 1 April 2018 / Accepted: 2 April 2018 / Published: 9 April 2018
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Abstract
Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of 16 cultivars of the
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Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of 16 cultivars of the tidal swamp rice, consisting of 15 from the South Kalimantan Provinces and 1 from South Sumatera, Indonesia (an outgroup) were analyzed phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice. On a nucleotide level, the tidal swamp rice showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that the tidal swamp rice has the unique phylogenetic trees, particularly for the combined sequence datasets. This information would be useful for the rice conservation and breeding programs in the future. Full article
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Open AccessArticle Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing
Diversity 2018, 10(2), 23; https://doi.org/10.3390/d10020023
Received: 29 March 2018 / Revised: 8 April 2018 / Accepted: 9 April 2018 / Published: 11 April 2018
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Abstract
Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for the molecular characterization of plant germplasm with complex and unsequenced genomes. This study represents the first preliminary effort using GBS to discover genome-wide genetic variants of northern wheatgrass (Elymus
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Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for the molecular characterization of plant germplasm with complex and unsequenced genomes. This study represents the first preliminary effort using GBS to discover genome-wide genetic variants of northern wheatgrass (Elymus lanceolatus ssp. lanceolatus (Scribn. and J. G. Sm.) Gould) plants and to assess the genetic diversity present in four cultivated and six wild accessions. The effort generated the first novel set of genomic resources and 5659 single nucleotide polymorphism (SNP) markers for this tetraploid grass. The diversity analysis revealed 8.8% of SNP variation residing among the 10 accessions and 1.9% SNP variation present between cultivated and wild accessions. The Bayesian analysis identified three major clusters of the assayed samples, and the principal coordinates analysis revealed the genetic distinctness of the two accessions collected from Nevada and Wyoming. The flow cytometry analysis confirmed the tetraploid nature of some of the assayed samples and estimated the average genome size to be 9.3–9.4 Gb for this species. These findings are useful for the genetic improvement of this native grass species for forage production and rangeland reclamation. The findings are also encouraging for the broad application of genotyping-by-sequencing in the characterization of genome-wide genetic variability in non-model polyploid plants. Full article
(This article belongs to the Special Issue Feature Papers for Celebrating the tenth Founding Year of Diversity)
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Open AccessArticle Influence of a Large Lake on the Winter Range of a Small Mammal: Lake Michigan and the Silver-Haired Bat (Lasionycteris noctivagans)
Diversity 2018, 10(2), 24; https://doi.org/10.3390/d10020024
Received: 11 March 2018 / Revised: 10 April 2018 / Accepted: 14 April 2018 / Published: 17 April 2018
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Abstract
We examine factors affecting the winter range limit of a migrating mammal, the silver-haired bat (Lasionycteris noctivagans), in states surrounding Lake Michigan, the fourth largest freshwater lake in the world. Using 555 citizen-based captures gathered between 1977 and 2016, we show
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We examine factors affecting the winter range limit of a migrating mammal, the silver-haired bat (Lasionycteris noctivagans), in states surrounding Lake Michigan, the fourth largest freshwater lake in the world. Using 555 citizen-based captures gathered between 1977 and 2016, we show that silver-haired bats overwinter (December–February) as far north as the 45th parallel, in areas roughly demarcated by the −12.2 °C (10 °F) mean daily minimum isotherm for January. Although summering populations adjacent to the lake are dominated by males, wintering animals are predominantly female and presumably migrants from north of Lake Superior. Logistic regression suggests that silver-haired bats are more likely to overwinter in warm areas, in counties near the lake, in urbanized locales, and on the west side of the lake. We believe that these small-bodied, solitary bats are hibernating in buildings and that use of human-made structures has allowed the silver-haired bat to overwinter in regions that are devoid of mines, caves and rock crevices and that are too cold for successful hibernation in trees. Lake Michigan impacts where this animal overwinters, presumably through the moderating influence of the lake on multiple aspects of the surrounding climate and because the shoreline likely is a major migratory pathway. Full article
(This article belongs to the Special Issue Diversity and Conservation of Bats)
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Open AccessArticle Genetic, Bio-Agronomic, and Nutritional Characterization of Kale (Brassica Oleracea L. var. Acephala) Diversity in Apulia, Southern Italy
Diversity 2018, 10(2), 25; https://doi.org/10.3390/d10020025
Received: 2 March 2018 / Revised: 11 April 2018 / Accepted: 13 April 2018 / Published: 17 April 2018
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Abstract
Kale (Brassica oleracea L. var. acephala) is a widely appreciated vegetable with a century-old history of cultivation in Italy. The present study was addressed to the collection and characterization of kale germplasm traditionally cultivated in Apulia, Southern Italy, nowadays at risk
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Kale (Brassica oleracea L. var. acephala) is a widely appreciated vegetable with a century-old history of cultivation in Italy. The present study was addressed to the collection and characterization of kale germplasm traditionally cultivated in Apulia, Southern Italy, nowadays at risk of genetic erosion. In total, nineteen Apulian kale accessions were acquired. Genotyping by means of simple sequence repeat (SSR) DNA markers led to the identification of highly informative primer combinations and highlighted significant patterns of molecular variation among accessions. Consistently, significant differences were observed with respect to morpho-agronomic traits, including yield and harvesting time, and the content of bioactive compounds, namely total phenols, flavonoids, and anthocyanins, associated with antioxidant activity. Overall, this study led to the establishment of an ex situ collection of great importance to preserve endangered Apulian kale germplasm and to provide seed access to potential growers. Meanwhile, it offers a first characterization of Apulian kale, useful to promote its consumption and valorisation through breeding programmes. Full article
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Open AccessArticle Cumulative Human Impacts on Coral Reefs: Assessing Risk and Management Implications for Brazilian Coral Reefs
Diversity 2018, 10(2), 26; https://doi.org/10.3390/d10020026
Received: 2 February 2018 / Revised: 17 April 2018 / Accepted: 17 April 2018 / Published: 24 April 2018
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Abstract
Effective management of coral reefs requires strategies tailored to cope with cumulative disturbances from human activities. In Brazil, where coral reefs are a priority for conservation, intensifying threats from local and global stressors are of paramount concern to management agencies. Using a cumulative
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Effective management of coral reefs requires strategies tailored to cope with cumulative disturbances from human activities. In Brazil, where coral reefs are a priority for conservation, intensifying threats from local and global stressors are of paramount concern to management agencies. Using a cumulative impact assessment approach, our goal was to inform management actions for coral reefs in Brazil by assessing their exposure to multiple stressors (fishing, land-based activities, coastal development, mining, aquaculture, shipping, and global warming). We calculated an index of the risk to cumulative impacts: (i) assuming uniform sensitivity of coral reefs to stressors; and (ii) using impact weights to reflect varying tolerance levels of coral reefs to each stressor. We also predicted the index in both the presence and absence of global warming. We found that 16% and 37% of coral reefs had high to very high risk of cumulative impacts, without and with information on sensitivity respectively, and 42% of reefs had low risk to cumulative impacts from both local and global stressors. Our outputs are the first comprehensive spatial dataset of cumulative impact on coral reefs in Brazil, and show that areas requiring attention mostly corresponded to those closer to population centres. We demonstrate how the relationships between risks from local and global stressors can be used to derive strategic management actions. Full article
(This article belongs to the Special Issue Climate Change and Human Activities on Coral Reefs)
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Open AccessArticle Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?
Diversity 2018, 10(2), 27; https://doi.org/10.3390/d10020027
Received: 11 February 2018 / Revised: 28 March 2018 / Accepted: 20 April 2018 / Published: 26 April 2018
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Abstract
Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic
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Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana) in three areas in Brazil, using inter-simple sequence repeat (ISSR) markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem. Full article
(This article belongs to the Special Issue Mangrove Ecology and Conservation)
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Open AccessArticle Review of Cape Verde Aphanommata Wollaston, 1873 (Coleoptera: Curculionidae: Cossoninae) with Description of New Species, Larva and Notes on Biology and Distributional Patterns
Diversity 2018, 10(2), 28; https://doi.org/10.3390/d10020028
Received: 29 March 2018 / Revised: 17 April 2018 / Accepted: 21 April 2018 / Published: 28 April 2018
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Abstract
The genus Aphanommata in the Old World is reviewed. Aphanommata kuscheli sp. nov. from São Nicolau and A. strakai sp. nov. from Fogo (both Cape Verde islands) are described. Aphanommata euphorbiarum (Wollaston, 1867) from Santo Antão in the Cape Verde islands is
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The genus Aphanommata in the Old World is reviewed. Aphanommata kuscheli sp. nov. from São Nicolau and A. strakai sp. nov. from Fogo (both Cape Verde islands) are described. Aphanommata euphorbiarum (Wollaston, 1867) from Santo Antão in the Cape Verde islands is redescribed and its lectotype is designated. All three Aphanommata species from the Cape Verde islands as well as A. filum (Mulsant and Rey, 1859) from Old World are diagnosed, illustrated, and keyed. Mature larva of A. kuscheli sp. nov. is described, larval morphology is discussed and the current state of knowledge about immature stages of Cossoninae is summarized. Vertical and inter-insular distributional pattern of Cape Verde Aphanommata and Pselactus is reviewed and discussed. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessArticle Restoration of Legacy Trees as Roosting Habitat for Myotis Bats in Eastern North American Forests
Diversity 2018, 10(2), 29; https://doi.org/10.3390/d10020029
Received: 8 March 2018 / Revised: 17 April 2018 / Accepted: 25 April 2018 / Published: 28 April 2018
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Abstract
Most eastern North American Myotis roost in forests during summer, with species forming maternity populations, or colonies, in cavities or crevices or beneath the bark of trees. In winter, these bats hibernate in caves and are experiencing overwinter mortalities due to infection from
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Most eastern North American Myotis roost in forests during summer, with species forming maternity populations, or colonies, in cavities or crevices or beneath the bark of trees. In winter, these bats hibernate in caves and are experiencing overwinter mortalities due to infection from the fungus Pseudogymnoascus destructans, which causes white-nose syndrome (WNS). Population recovery of WNS-affected species is constrained by the ability of survivors to locate habitats suitable for rearing pups in summer. Forests in eastern North America have been severely altered by deforestation, land-use change, fragmentation and inadvertent introduction of exotic insect pests, resulting in shifts in tree distributions and loss of large-diameter canopy-dominant trees. This paper explores patterns in use of tree roosts by species of Myotis across Canada and the United States using meta-data from published sources. Myotis in western Canada, the Northwest, and Southwest selected the largest diameter roost trees and also supported the largest maximum exit counts. Myotis lucifugus, M. septentrionalis and M. sodalis, three species that inhabit eastern forests and which are currently experiencing region-wide mortalities because of WNS, selected roosts with the smallest average diameters. Recovery efforts for bark- and cavity-roosting Myotis in eastern North American forests could benefit from management that provides for large-diameter trees that offer more temporally-stable structures for roosting during the summer maternity season. Full article
(This article belongs to the Special Issue Diversity and Conservation of Bats)
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Open AccessArticle The Enigmatic Weevil Genus Philetaerobius from Southern Africa: Definition, Affinities and Description of Three New Species (Coleoptera: Curculionidae: Entiminae)
Diversity 2018, 10(2), 30; https://doi.org/10.3390/d10020030
Received: 7 March 2018 / Revised: 17 April 2018 / Accepted: 21 April 2018 / Published: 1 May 2018
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Abstract
The small entimine genus Philetaerobius Marshall, 1923 is revised, entailing a redescription of the genus and the only hitherto described species, P. nidicola Marshall, as well as the description of three new species, P. endroedyi sp. n., P. garibebi sp. n. and P.
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The small entimine genus Philetaerobius Marshall, 1923 is revised, entailing a redescription of the genus and the only hitherto described species, P. nidicola Marshall, as well as the description of three new species, P. endroedyi sp. n., P. garibebi sp. n. and P. louwi sp. n. A lectotype is designated for P. nidicola Marshall. The habitus and taxonomically important structures of all species are illustrated, including the previously unrecorded male and female genitalia. A key to the four species is provided, as well as a map of their known distributions in southern Namibia and the Northern and Western Cape provinces of South Africa. The habits of the genus, as known, are summarized, and its taxonomic position and indicated relationship with the taxonomically equally isolated genus Spartecerus are discussed. The habitus and genitalia of some Spartecerus species are also illustrated, and the available information on the life-history of the genus is summarized. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessArticle Patterns of Long-Term Population Trends of Three Lupine-Feeding Butterflies in Wisconsin
Diversity 2018, 10(2), 31; https://doi.org/10.3390/d10020031
Received: 5 February 2018 / Revised: 11 April 2018 / Accepted: 13 April 2018 / Published: 4 May 2018
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Abstract
We monitored consecutive generations of three lupine-feeding specialist butterflies in pine-oak barrens in central Wisconsin, USA: Frosted Elfin (Callophrys irus), Karner Blue (Lycaeides melissa samuelis), and Persius Duskywing (Erynnis persius) during 1991–2014. We also monitored the summer
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We monitored consecutive generations of three lupine-feeding specialist butterflies in pine-oak barrens in central Wisconsin, USA: Frosted Elfin (Callophrys irus), Karner Blue (Lycaeides melissa samuelis), and Persius Duskywing (Erynnis persius) during 1991–2014. We also monitored the summer generation of Karner Blues in northwestern Wisconsin. We present results on 24 sites for Frosted Elfin and Persius Duskywing, and 39 sites for Karner Blue. Land uses in sites occupied by the federally endangered Karner Blue are regulated. Economically utilized lands classified as “Shifting Mosaic” (SM) (forestry land) or “Permanency of Habitat” (PH) (rights-of-way) are afforded a lower standard of conservation results than the more favorable management expected of Reserves (R). For all three species, reserve sites had more favorable trends than permanency of habitat and shifting mosaic sites. Frosted Elfin and Persius Duskywing had more strongly negative trends in permanency of habitat than shifting mosaic, but vice versa for Karner Blue. Shifting mosaic sites added more recently to the study had negative trends, but not as strongly as longer-monitored shifting mosaic sites. Another large shifting mosaic complex (Hunter Haven), monitored in 17 years during 1995–2014 for Frosted Elfin and Persius Duskywing, had non-negative trends. Individual reserve sites also had more favorable trends than collectively for all reserve sites, including significant positive trends for Persius Duskywing and Karner Blue, and a stable trend for Frosted Elfin. Thus, land use is implicated not only for declines but also for effective conservation of these species. Full article
(This article belongs to the Special Issue Butterfly Conservation)
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Open AccessArticle Anthropogenic Impacts on Coral Reef Harpacticoid Copepods
Diversity 2018, 10(2), 32; https://doi.org/10.3390/d10020032
Received: 20 February 2018 / Revised: 27 April 2018 / Accepted: 30 April 2018 / Published: 4 May 2018
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Abstract
The number of studies demonstrating the susceptibility of benthic reef communities to anthropogenic impacts is growing. However, for some of the components of reef fauna, such as meiobenthic harpacticoid copepods, information is still lacking. Here, different diversity and taxonomic distinctness indexes and multivariate
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The number of studies demonstrating the susceptibility of benthic reef communities to anthropogenic impacts is growing. However, for some of the components of reef fauna, such as meiobenthic harpacticoid copepods, information is still lacking. Here, different diversity and taxonomic distinctness indexes and multivariate analyses were used to test whether the assemblage of harpacticoid copepods colonizing Artificial Substrate Units (ASUs) is an appropriate tool for the identification of reefs subjected to different levels of anthropogenic pressure. Furthermore, we also evaluate if diffused, persistent, anthropogenic impacts generate the homogenization and simplification of Harpacticoida assemblages. Six reefs were organized into two groups along the coast, depending on their proximity to very large urban centers. ASUs were used for meiofauna colonization and, for each reef, 320 Harpacticoida individuals were separated for identification at the species level. Abiotic parameters were analyzed, and significant differences were found between the two groups of reefs, with an increase in dissolved inorganic nutrients found in areas near large urban centers. Both the multivariate analyses and the indexes of diversity showed a clear separation between the reefs closer to the urban zones and those further away, as a response to the anthropogenic pressure. As hypothesized, in the impacted reef areas, there was a strong simplification and homogenization of the harpacticoid copepod assemblages. However, the results of the indexes, based on taxonomic distinctness, suggest that there was no phylogenetic signal of anthropogenic impact on coral reef harpacticoid copepods. Full article
(This article belongs to the Special Issue Climate Change and Human Activities on Coral Reefs)
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Open AccessArticle Unveiling the History of a Peculiar Weevil-Plant Interaction in South America: A Phylogeographic Approach to Hydnorobius hydnorae (Belidae) Associated with Prosopanche americana (Aristolochiaceae)
Diversity 2018, 10(2), 33; https://doi.org/10.3390/d10020033
Received: 28 March 2018 / Revised: 1 May 2018 / Accepted: 4 May 2018 / Published: 6 May 2018
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Abstract
Interspecific interactions take place over both long and short time-frames. However, it is not completely understood if the interacting-partners persisted, migrated, or expanded in concert with Quaternary climate and landscape changes. We aim to understand whether there is concordance between the specialist weevil
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Interspecific interactions take place over both long and short time-frames. However, it is not completely understood if the interacting-partners persisted, migrated, or expanded in concert with Quaternary climate and landscape changes. We aim to understand whether there is concordance between the specialist weevil Hydnorobius hydnorae and its parasitic host plant, Prosopanche americana in space and time. We aim to determine whether Prosopanche had already established its range, and Hydnorobius later actively colonized this rare resource; or, if both host plant and herbivore expanded their range concomitantly. We performed population genetic, phylogeographic and Bayesian diffusion analysis of Cytochrome B sequences from 18 weevil localities and used paleodistribution models to infer host plant dispersal patterns. We found strong but uneven population structure across the range for H. hydnorae with weak signals of population growth, and haplotype network structure and SAMOVA groupings closely following biogeographic region boundaries. The ancestral areas for both Hydnorobius and Prosopanche are reconstructed in San Luis province within the Chaco Biogeographic province. Our results indicate a long trajectory of host-tracking through space and time, where the weevil has expanded its geographic range following its host plant, without significant demographic growth. We explore the past environmental changes that could underlie the boundaries between locality groups. We suggest that geographic dispersal without population growth in Hydnorobius could be enabled by the scarcity of the host plant itself, allowing for slow expansion rates and stable populations, with no need for significant demographic growth pulses to support range expansion. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessArticle On the Phylogenetic Position of the Weevil Tribe Acentrusini Alonso-Zarazaga, 2005 (Coleoptera: Curculionidae: Curculioninae)
Diversity 2018, 10(2), 34; https://doi.org/10.3390/d10020034
Received: 26 March 2018 / Revised: 1 May 2018 / Accepted: 4 May 2018 / Published: 7 May 2018
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Abstract
Based on intrinsic morphological and extrinsic bionomic characters, the systematic position of the weevil tribe Acentrusini Alonso-Zarazaga, 2005 (Coleoptera: Curculionidae: Curculioninae) was determined. Maximum parsimony and Bayesian inference as well as nonmetric multi-dimensional scaling were used to analyze 34 morphological characters of adults,
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Based on intrinsic morphological and extrinsic bionomic characters, the systematic position of the weevil tribe Acentrusini Alonso-Zarazaga, 2005 (Coleoptera: Curculionidae: Curculioninae) was determined. Maximum parsimony and Bayesian inference as well as nonmetric multi-dimensional scaling were used to analyze 34 morphological characters of adults, complemented by four host plant characters associated with particular weevil tribes. Sixteen species belonging to two subfamilies (Brachycerinae, Curculionidae) and seven tribes (Acentrusini, Anthonomini, Ellescini, Erirhinini, Smicronychini, Storeini, Styphlini) of the family Curculionidae and one outgroup species (Attelabidae) were studied. Phylogenetic and multi-dimensional analyses revealed the tribe Smicronychini as most closely related to Acentrusini. Of the tribes of Curculioninae studied, Styphlini, Anthonomini and Ellescini showed a certain degree of phylogenetic relation to Acentrusini, whereas Storeini were found to be least related. Full article
(This article belongs to the Special Issue Systematics and Phylogeny of Weevils)
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Open AccessArticle Correlated Effects of Ocean Acidification and Warming on Behavioral and Metabolic Traits of a Large Pelagic Fish
Diversity 2018, 10(2), 35; https://doi.org/10.3390/d10020035
Received: 30 March 2018 / Revised: 1 May 2018 / Accepted: 3 May 2018 / Published: 8 May 2018
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Abstract
Ocean acidification and warming are co-occurring stressors, yet their effects on early life stages of large pelagic fishes are not well known. Here, we determined the effects of elevated CO2 and temperature at levels projected for the end of the century on
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Ocean acidification and warming are co-occurring stressors, yet their effects on early life stages of large pelagic fishes are not well known. Here, we determined the effects of elevated CO2 and temperature at levels projected for the end of the century on activity levels, boldness, and metabolic traits (i.e., oxygen uptake rates) in larval kingfish (Seriola lalandi), a large pelagic fish with a circumglobal distribution. We also examined correlations between these behavioral and physiological traits measured under different treatments. Kingfish were reared from the egg stage to 25 days post-hatch in a full factorial design of ambient and elevated CO2 (~500 µatm and ~1000 µatm) and temperature (21 °C and 25 °C). Activity levels were higher in fish from the elevated temperature treatment compared with fish reared under ambient temperature. However, elevated CO2 did not affect activity, and boldness was not affected by either elevated CO2 or temperature. Both elevated CO2 and temperature resulted in increased resting oxygen uptake rates compared to fish reared under ambient conditions, but neither affected maximum oxygen uptake rates nor aerobic scope. Resting oxygen uptake rates and boldness were negatively correlated under ambient temperature, but positively correlated under elevated temperature. Maximum oxygen uptake rates and boldness were also negatively correlated under ambient temperature. These findings suggest that elevated temperature has a greater impact on behavioral and physiological traits of larval kingfish than elevated CO2. However, elevated CO2 exposure did increase resting oxygen uptake rates and interact with temperature in complex ways. Our results provide novel behavioral and physiological data on the responses of the larval stage of a large pelagic fish to ocean acidification and warming conditions, demonstrate correlations between these traits, and suggest that these correlations could influence the direction and pace of adaptation to global climate change. Full article
(This article belongs to the Special Issue Impacts of Ocean Acidification on Marine Fishes)
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Open AccessArticle Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity
Diversity 2018, 10(2), 36; https://doi.org/10.3390/d10020036
Received: 17 April 2018 / Revised: 2 May 2018 / Accepted: 10 May 2018 / Published: 14 May 2018
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Abstract
The Australian monsoonal tropics (AMT) is a significant biodiversity hotspot, and recent genetic studies of several vertebrate groups have revealed its level of diversity is far higher than previously thought. However, the extent to which this applies to the AMT’s insect fauna, which
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The Australian monsoonal tropics (AMT) is a significant biodiversity hotspot, and recent genetic studies of several vertebrate groups have revealed its level of diversity is far higher than previously thought. However, the extent to which this applies to the AMT’s insect fauna, which represents most AMT faunal species, remains unknown. Here we examine the extent of unrecognised diversity in the AMT’s ecologically dominant insect group, ants. We used CO1 barcoding in combination with morphological variation and geographic distribution to explore diversity within seven taxa currently recognised as single species occurring throughout the AMT: one species of Papyrius Shattuck 1992, one of Iridomyrmex Mayr 1862, two from the Cardiocondyla nuda (Mayr 1866) group, and three from the Camponotus novaehollandiae (Mayr 1870) group. We found six of the seven target species each to represent several species, based on a combination of CO1 divergence (ranging up to 13%), morphological differentiation and geographic distribution. Our findings indicate that the levels of diversity and endemism of the AMT ant fauna are far higher than currently realised. We urge the need for further research in insect biodiversity in the AMT, both for a better understanding of the evolution of its remarkable biota, and as a basis for improved conservation planning. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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Open AccessFeature PaperReview The Functional Impact of Transposable Elements on the Diversity of Plant Genomes
Diversity 2018, 10(2), 18; https://doi.org/10.3390/d10020018
Received: 28 February 2018 / Revised: 19 March 2018 / Accepted: 21 March 2018 / Published: 22 March 2018
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Abstract
Transposable elements (TEs) are self-mobilized DNA sequences that constitute a large portion of plant genomes. Being selfish DNA, they utilize different mobilization mechanisms to persist and proliferate in host genomes. It is important that new TE insertions generate de novo variability, most of
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Transposable elements (TEs) are self-mobilized DNA sequences that constitute a large portion of plant genomes. Being selfish DNA, they utilize different mobilization mechanisms to persist and proliferate in host genomes. It is important that new TE insertions generate de novo variability, most of which is likely to be deleterious, but some can be advantageous. Also, a growing body of evidence shows that TEs were continually recruited by their hosts to provide additional functionality. Here, we review potential ways in which transposable elements can provide novel functions to host genomes, from simple gene knock-outs to complex rewiring of gene expression networks. We discuss possible implications of TE presence and activity in crop genomes for agricultural production. Full article
(This article belongs to the Special Issue Feature Papers for Celebrating the tenth Founding Year of Diversity)
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