The cosmopolitan echiniscid genus Hypechiniscus contains exclusively rare species. In this contribution, by combining statistical morphometry and molecular phylogeny, we present qualitative and quantitative aspects of Hypechiniscus diversity, which remained hidden under the two purportedly cosmopolitan species: H. gladiator and H. exarmatus. A neotype is designated for H. gladiator from Creag Meagaidh (Scotland), and an informal re-description is provided for H. exarmatus based on animals from Creag Meagaidh and the Isle of Skye (Inner Hebrides). Subspecies/forms of H. gladiator are suppressed due to the high developmental variability of the cirrus dorsalis. At the same time, four species of the genus are described: H. daedalus sp. nov. from Roan Mountain and the Great Smoky Mountains (Southern Appalachian Mountains, USA), H. flavus sp. nov. and H. geminus sp. nov. from the Yatsugatake Mountains (Honshu, Japan), and H. cataractus sp. nov. from the Malay Archipelago (Borneo and the Moluccas). Dorsal and ventral sculpturing, together with morphometric traits, are shown to be the key characters that allow for the phenotypic discrimination of species within the genus. Furthermore, the morphology of Hypechiniscus is discussed and compared to that of the most similar genera, Pseudechiniscus and Stellariscus. Finally, a diagnostic key to all recognized Hypechiniscus species is provided.

During European settlement, the vast majority of grasslands in Illinois were converted for agricultural purposes. Some of the remaining natural areas in southern Illinois include natural xeric forest openings (i.e., barrens, glades, outcrops), that have transitional community compositions representative of previously extensive grasslands and adjacent hardwood forests. Previous research in these forest openings show that the communities are largely driven by edaphic conditions and vary spatially across southern Illinois. While most of these communities are currently protected and established as nature preserves, threats to these natural xeric forest openings continue to persist, such as climate change and exotic invasion. These threats are capable of altering taxonomic, phylogenetic, and functional diversity and community composition. The overall goals of this research were to 1) determine metapopulations and metacommunity structure in a local group of sandstone outcrop communities (a subset of natural xeric forest opening communities), 2) expand resolution to a regional scale to include natural xeric forest openings with several substrates to investigate changes in taxonomic, phylogenetic, and functional diversity and community composition since surveys conducted in 1988, and 3) include spatial analyses to characterize autocorrelation structure of diversity and environmental variables and biological turnover of natural xeric forest openings at a global scale. Sandstone outcrop communities at Jackson Hollow in Pope County, Illinois had several metapopulation species based on Hanski’s incidence functional model. These metapopulation species were more often members of the Asteraceae and Poaceae than members of other plant families, and were often exotic in origin with short-lived lifecycles. These metapopulation species were also neither dominant species or singletons within sandstone patches. Based on the Elements of Metacommunity (EMS) Framework, positive coherence, species turnover, and boundary clumping indicate that these sandstone outcrop communities are predictable communities where species replace one each other regularly as groups of species and respond similarly to environmental gradients. Furthermore, diversity metrics were all positively correlated with each other, but not with patch characteristics. In addition, total species and metapopulation species were positively associated with phylogenetic and functional diversity, but metapopulation species were positively associated with non-standardized phylogenetic and functional indices. When looking at several natural xeric forest openings across southern Illinois and comparing them based on substrate types and between surveys in 1988 and 2019, taxonomic, phylogenetic, and functional compositions were distinct based on substrates, but were stable and resilient across surveys. Sandstone and shale communities were the most similar based on composition, followed by limestone communities compared to sandstone and shale communities, and then loess communities being the most dissimilar from all other communities. Environmental variables that best explained differences in community composition were canopy cover, soil acidity, photosynthetically active radiation, and soil depth. Diversity variables that best explained differences in community composition were phylogenetic nearest taxon index, Faith’s phylogenetic diversity, and dominant species richness. Ninety-four different species were either significant indicators for specific substrates, or 2019 surveys. While no cases of phylogenetic signal were observed based on functional traits, substrate types, or surveys, three cases of functional signal based on dominant communities were observed in sandstone communities in 2019, shale communities in 2019, and overall shale communities across 1988 and 2019 surveys. When applying spatial analyses to these natural xeric forest openings to understand autocorrelation structure and biological turnover, soil depth was the only environmental variable that exhibited significant spatial autocorrelation, as previous glacial events caused loess hill prairies in the northwestern extent of this study to have deeper soil due to Quaternary loess deposition. However, several diversity metrics exhibited spatial structure based on 1988 and 2019 surveys (1988: dominant species richness, Pielou’s evenness, Shannon-Weiner diversity, Faith’s phylogenetic diversity, and distance-based functional diversity; 2019: dominant species richness, Pielou’s evenness, Shannon-Weiner diversity, Faith’s phylogenetic diversity, and phylogenetic nearest taxon index). In addition, climate variables daily mean temperature and total annual precipitation exhibited spatial structure. Most variables were spatially clustered at local site scales and spatially dispersed at larger scales and spatially over-dispersed at a regional scale. Generalized dissimilarity models constructed based on elevation, soil, and climate variables showed that models based on both functional composition and 2019 surveys best explained biological turnover compared to taxonomic and phylogenetic and 1988 models. Several variables included in models differed based on aspects of biological turnover or surveys, but temperature annual range and soil bulk density variables were common across all models. However, differences between total deviance explained and null deviances show that geographic distance between natural xeric forest openings was overwhelmingly the most influential variable contributing to biological turnover. Given these observations, natural xeric forest openings at local scales persist as distinct habitat patches amidst a landscape that largely constitutes an inhospitable matrix to colonizing species, yet certain species are able to migrate between patches. The resulting community assembly of individual patches is determined by both colonizing species and environmental gradients across the landscape. Despite simultaneous threats to diversity and composition in natural xeric forest openings at a regional scale, substrate continues to drive community assembly, in that certain species are characteristic indicators of these substrates. Furthermore, the most recent surveys in sandstone and shale communities exhibited functional signals. However, these natural xeric forest openings are spatially structured based on soil depth due to glacial history, certain metrics of diversity, and climate variables. Along with these occurrences of spatial autocorrelations, different aspects of biological turnover are best predicated by geographic distance as well as unique combinations of climate and soil variables between different aspects of diversity and surveys.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24457号 / 理博第4956号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 中野 隆文, 教授 本川 雅治, 教授 森 哲 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

The last decade has seen great advances in Next-Generation Sequencing technologies, and, as a result, there has been a rise in the number of genomes sequenced each year. In 2017, there were as many as 10,000 new organisms sequenced and added into the RefSeq Database. Taxonomy prediction is a science involving the hierarchical classification of DNA fragments up to the rank species. In this research, we introduce Predicting Linked Organisms, Plinko, for short. Plinko is a fully-functioning, state-of-the-art predictive system that accurately captures DNA - Taxonomy relationships where other state-of-the-art algorithms falter. Plinko leverages multi-view convolutional neural networks and the pre-defined taxonomy tree structure to improve multi-level taxonomy prediction. In the Plinko strategy, each network takes advantage of different word usage patterns corresponding to different levels of evolutionary divergence. Plinko has the advantages of relatively low storage, GPGPU parallel training and inference, making the solution portable, and scalable with anticipated genome database growth. To the best of our knowledge, Plinko is the first to use multi-view convolutional neural networks as the core algorithm in a compositional,alignment-free approach to taxonomy prediction. / Master of Science / Taxonomy prediction is a science involving the hierarchical classification of DNA fragments up to the rank species. Given species diversity on Earth, taxonomy prediction gets challenging with (i) increasing number of species (labels) to classify and (ii) decreasing input (DNA) size. In this research, we introduce Predicting Linked Organisms, Plinko, for short. Plinko is a fully-functioning, state-of-the-art predictive system that accurately captures DNA - Taxonomy relationships where other state-of-the-art algorithms falter. Three major challenges in taxonomy prediction are (i) large dataset sizes (order of 109 sequences) (ii) large label spaces (order of 103 labels) and (iii) low resolution inputs (100 base pairs or less). Plinko leverages multi-view convolutional neural networks and the pre-defined taxonomy tree structure to improve multi-level taxonomy prediction for hard to classify sequences under the three conditions stated above. Plinko has the advantage of relatively low storage footprint, making the solution portable, and scalable with anticipated genome database growth. To the best of our knowledge, Plinko is the first to use multi-view convolutional neural networks as the core algorithm in a compositional, alignment-free approach to taxonomy prediction.

Bioassessment is the concept of evaluating the ecological condition of habitats by surveying the resident assemblages of living organisms. Conducting bioassessment with benthic macroinvertebrates is still evolving and continues to be refined. There are strongly divided opinions about study design, sampling methods, laboratory analyses, and data analysis. Two issues that are currently being debated about study design for bioassessment in streams were examined here: 1) what habitats within streams should be sampled; 2) and is it necessary to identify organisms to the species level? The influence of habitat sampling design and level of taxonomic identification on the interpretation of ecological conditions of ten small streams in western Virginia was examined. Cattle watering and grazing heavily affected five of these streams (impaired sites). The other five streams, with no recent cattle activity or other impact by man, were considered to be reference sites because they were minimally impaired and represented best attainable conditions. Inferential and non-inferential statistical analyses concluded that multiple habitat sampling design was more effective than a single habitat design (riffle only) at distinguishing impaired conditions, regardless of taxonomic level. It appeared that sampling design (riffle habitat versus multiple habitats) is more important than taxonomic identification level for distinguishing reference and impaired ecological conditions in this bioassessment study. All levels of taxonomic resolution, which were studied, showed that the macroinvertebrate assemblages at the reference and impaired sites were very different and the assemblages at the impaired sites were adversely affected by perturbation. This study supported the sampling of multiple habitats and identification to the family level as a design for best determining the ecological condition of streams in bioassessment. / Master of Science

Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-08-17T17:25:58Z No. of bitstreams: 1 FernandoOliveira.pdf: 2347086 bytes, checksum: 0b2d54b7d13b7467bee9db13f63100f5 (MD5) / Made available in DSpace on 2017-08-17T17:25:58Z (GMT). No. of bitstreams: 1 FernandoOliveira.pdf: 2347086 bytes, checksum: 0b2d54b7d13b7467bee9db13f63100f5 (MD5) Previous issue date: 2013-02-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Breast cancer is the second most common type of cancer in the world and difficult to diagnose. Distinguished Systems Aided Detection and Diagnosis Computer have been used to assist experts in the health field with an indication of suspicious areas of difficult perception to the human eye, thus aiding in the detection and diagnosis of cancer. This dissertation proposes a methodology for discrimination and classification of regions extracted from the breast mass and non-mass. The Digital Database for Screening Mammography (DDSM) is used in this work for the acquisition of mammograms, which are extracted from the regions of mass and non-mass. The Taxonomic Diversity Index (∆) and the Taxonomic Distinctness (∆*) are used to describe the texture of the regions of interest, originally applied in ecology. The calculation of those indices is based on phylogenetic trees, which applied in this work to describe patterns in regions of the images of the breast with two regions bounding approaches to texture analysis: circle with rings and internal with external masks. Suggested in this work to be applied in the description of patterns of regions in breast imaging approaches circle with rings and masks as internal and external boundaries regions for texture analysis. Support Vector Machine (SVM) is used to classify the regions in mass or non-mass. The proposed methodology provides successful results for the classification of masses and non-mass, reaching an average accuracy of 99.67%. / O câncer de mama é o segundo tipo de câncer mais frequente no mundo e de difícil diagnóstico. Distintos Sistemas de Detecção e Diagnóstico Auxiliados por Computador (Computer Aided Detection/Diagnosis) têm sido utilizados para auxiliar especialistas da área da saúde com a indicação de áreas suspeitas de difícil percepção ao olho humano, assim ajudando na detecção e diagnóstico de câncer. Este trabalho propõe uma metodologia de discriminação e classificação de regiões extraídas da mama em massa e não-massa. O banco de imagens Digital Database for Screening Mammography (DDSM) é usado neste trabalho para aquisição das mamografias, onde são extraído as regiões de massa e não-massa. Na descrição da textura da região de interesse são utilizados os Índices de Diversidade Taxonômica (∆) e Distinção Taxonômica (∆*), provenientes da ecologia. O cálculo destes índices é baseado nas árvores filogenéticas, sendo aplicados neste trabalho na descrição de padrões em regiões das imagens da mama com duas abordagens de regiões delimitadoras para análise da textura: círculo com anéis e máscaras internas com externas. Para classificação das regiões em massa e não-massa é utilizado o classificador Máquina de Vetores de Suporte (MVS). A metodologia apresenta resultados promissores para a classificação de massas e não-massas, alcançando uma acurácia média de 99,67%.

<p>Redeterminacijom publikovanog i determinacijom novog materijala iz podfamilije Syrphinae na području Srbije su zabeležene 134 vrste iz 25 rodova. Sedam vrsta (<em>Chrysotoxum orthostylus </em>Vujić, in prep., <em>Chrysotoxum </em>aff.<em> festivum</em>, <em>Chrysotoxum </em>aff. <em>vernale, Dasysyrphus laskai</em> Doczkal &amp; St&aring;hls, in prep., <em>Melanostoma</em> aff.<em> mellinum, Paragus rarus</em> Vujić et al., in prep. i <em>Xanthogramma citrofasciatum </em>B Doczkal, in prep.) su nove za nauku i njihovi opisi se nalaze u pripremi. 14 vrsta su nove za faunu Balkanskog poluostrva, dok su 39 nove za faunu Srbije (uključujući i one koje su nove za Balkan).</p><p>Unutar vrste<em> Chrysotoxum festivum </em>uočena su dva fenotipa &bdquo;svetli&ldquo; i &bdquo;tamni&ldquo; koji se jasno razlikuju na osnovu niza morfolo&scaron;kih karaktera (&scaron;irina lica, &scaron;irina crne trake na licu, popra&scaron;enost čela, boja dlaka na mezonotumu i skutelumu, &scaron;irina oznaka na T2 i T3) kao i na osnovu veličine i oblika krila. Usled jasne divergencije pomenutih fenotipova kao i njihove simpatrije u pitanju su odvojene vrste.</p><p>Jasno izdvajanje fenotipova na osnovu morfolo&scaron;kih karaktera odraslih jedinki uključujući i parametre krila (veličinu i oblik) ustanovljeno je i unutar vrsta <em>Chrysotoxum vernale</em> i <em>Melanostoma mellinum.</em> Unutar vrste <em>Chrysotoxum vernale</em> se izdvajaju dva nezavisna taksona- <em>Chrysotoxum vernale</em> i <em>Chrysotoxum </em>aff. <em>vernale</em>, a unutar vrste <em>Melanostoma mellinum</em>- <em>Melanostoma mellinum </em>i<em> Melanostoma </em>aff. <em>mellinum</em>.</p><p>Zoogeografskom analizom je ustanovljeno da su najbrojnije vrste &scaron;irokog areala, koje čine čak 75,19% od ukupnog broja vrsta, 12 vrsta (9,02%) ima srednjeevropski, 10 severnoevropski (7,52%), a svega dve vrste (1,5%) južnoevropski tip areala. Dve vrste (1,5%) su ograničenog areala.</p><p>Dve vrste iz podfamilije <em>Syrphinae</em> spadaju u kategoriju strogo za&scaron;tićenih vrsta, dok pet spada u kategoriju za&scaron;tićenih vrsta na području Srbije (Uredbom Ministarstva za za&scaron;titu životne sredine i prostornog planiranja Republike Srbije od 2010. godine o za&scaron;titi strogo ugroženih i ugroženih divljih vrsta biljaka, životinja i gljiva). Razmatrajući status vrsta na evropskom nivou po Speight (2010) većina vrsta (118) pripada kategoriji neugroženih vrsta &bdquo;unthreatened&ldquo;, a po četiri kategoriji ugroženih vrsta &bdquo;threatened&ldquo; i vrsta čija se brojnost smanjuje &bdquo;decreasing&ldquo;.</p><p>Najvećim indeksom diverziteta (3,66) se odlikuje Duba&scaron;nica sa Malinikom, zatim slede Vr&scaron;ačke planine (H=3,62) i Kopaonik (H=3,59). Najniži indeks diverziteta imaju Bosilegrad (1,21) i dolina Tami&scaron;a (1,55) &scaron;to je i očekivano obzirom na broj sakupljenih primeraka i registrovanih vrsta.</p><p>Rad predstavlja sintezu faunističkih istraživanja vrsta iz podfamilije Syrphinae u Srbiji, taksonomsku analizu zabeleženih vrsta kao i razre&scaron;avanje taksonomskih problema unutar mnogih vrsta unutar kojih su oni bili prisutni.</p> / <p>This PhD thesis is about the taxonomic and faunistic revision of the Syrphinae hoverflies (Syrphidae) of Serbia. As a result of this study, 134 species of 25 genera were reported to Serbia. This account comprised seven species new to science: <em>Chrysotoxum orthostylus</em> Vujić, in prep.<em>Chryotoxum </em>aff. <em>festivum</em>, <em>Chrysotoxum</em> aff. <em>vernale</em>,&nbsp;<em> Dasysyrphus laskai</em> Doczkal &amp; St&aring;hls, in prep., <em>Melanostoma</em> aff. <em>mellinum</em>, <em>Paragus rarus</em>&nbsp;Vujić et al., in prep. and <em>Xanthogramma citrofasciatum</em> B Doczkal, in prep.. Additionally,&nbsp;&nbsp; 39 species were new to Serbia, 14 of them also new to the Balkan Peninsula.</p><p>A first approach to solve some taxonomic problems within three different hoverfly taxa is provided in this study. The examined material of <em>Chrysotoxum festivum</em> from Serbia exhibited two different phenotypes, &ldquo;light&rdquo; and &ldquo;dark&rdquo;. These phenotypes were defined by both landmark-based geometric morphometric characters of wings and other adult morphological characters (width of face, width of black stripe on face, frons pruinosity,colour of hairs on mesonotum and scutellum, width of stripes on terga 2 and 3, etc). The presented results together with the sympatry of the studied phenotypes suggested the&nbsp;&nbsp; existence of at least two different taxa within the species, currently known under the name <em>Chrysotoxum festivum</em>. Similarly, traditional characters in adult morphology and morphometric characters of wings (size and shape) showed the existence of two welldefined phenotypes both within the species <em>Chrysotoxum vernale</em> <em>(Chrysotoxum vernale</em> and <em>Chrysotoxum </em>aff. <em>vernale</em>) and the species <em>Melanostoma mellinum </em>(<em>Melanostoma mellinum </em>and <em>Melanostoma</em> aff. <em>mellinum</em>).</p><p>The zoogeographic analysis showed that most of the studied species are widespread in Europe (75,19%), and the rest of species are Central European (9,02%), Northern European (7,52%) or South European (1,5%).</p><p>At European level, 118 species are thought to be unthreatened, four threatened and four with decreasing populations according to the last version of Syrph the Net, the Database of European Syrphidae. In Serbia, two of the studied species are regarded as &ldquo;strictly protected&ldquo; and five as &ldquo;protected&ldquo; under the Regulation on the Promulgation and&nbsp;&nbsp; Protection of the Protected and Strictly Protected Wild Species of Plants, Animals and Fungi (Ministry of Environment and Spatial Planning, Serbia).</p><p>The localities of Duba&scaron;nica and Malinik have the highest values for the scored diversity index (H = 3.66), followed by Vr&scaron;ačke planine (H=3.62) and Kopaonik&nbsp; (H=3.59). Bosilegrad and Tami&scaron; have the lowest diversity values, 1.21 and 1.55 respectively, as it was expected by the low species richness and abundance of hoverflies recorded in these localities.</p>

Benthic macroinvertebrate diversity influences stream food web dynamics, nutrient cycling and material exchange between the benthos and the water column. Stream bioassessment has moved to the forefront of water quality monitoring in terms of benthic macroinvertebrate diversity in the recent past. The objectives of this study were to determine optimum subsample size and level of taxonomic resolution necessary to accurately and precisely describe macroinvertebrate diversity in streams flowing in the Piedmont province of the James River watershed in Virginia. Forty-nine sampling sites were selected from streams within the Piedmont Physiographic Province of the James River watershed. Ten sites were randomly selected to have all macroinvertebrates in the sample identified to the genus level whenever possible. Optimum subsampling intensities and Virginia Stream Condition Index (VSCI) metrics and scores were determined. For samples with the total number of individuals at less than 500, the genus level of taxonomy provided lower overall optimum subsampling intensities. However, for samples with total individuals over 1000, optimum subsampling intensities at the genus level of taxonomy were higher than the family level for more than 50% of the metrics. For both family and genus levels of taxonomy, the majority of optimum subsampling intensities were well over 50% of the total individuals in the sample, with some as high as 100% of the individuals. While optimum subsampling intensities were valuable in comparing family and genus level taxonomy, they are not reasonable for stream bioassessment protocols; the cost:benefit ratio would be highly unbalanced. A minimum subsample size of 200 individuals is optimum for determining VSCI scores, while optimum taxonomic resolution is dependent on several factors. Thus, the level of taxonomic resolution for a particular study should be determined by the study objectives, level of site impairment and sample size.

Sandy beaches are often highly allochthonous, depending on external subsidies of carbon and nutrients. Despite this, sandy beach macrofaunal assemblages have received little attention regarding their response to enhanced primary productivity generated from coastal upwelling. This thesis investigates the influence of upwelling on macrofaunal assemblages over a variety of spatial and temporal scales. Spatially, four regions were examined across two biogeographic provinces to remove temperature as a confounding factor, and limit biogeography-specific effects. A nested hierarchical design enabled both large and small scales to be examined and generalities about upwelling effects across multiple areas to be considered. Sampling was conducted in two seasons, and over two years, to test the persistence of any effects. Biogeography and region had the strongest influences on macrofaunal biodiversity. Upwelling influenced macrofaunal assemblages in every region when analyses were conducted at the species level. However, the particular effect, positive or negative, differed among regions depending on local factors, and between the response variables, abundance and biomass. Coarser scales of taxonomy, feeding guild and developmental mode were investigated; however, the influence of upwelling generally became weaker and more varied, and occasionally disappeared. Seasonality was greater on the South Coast but was still important in some analyses on the West Coast. At the small-scale, variation within-beaches was lower than between beaches, assemblage structure remained stable over time, and consistent zonation was not present. The influence of temperature on filtration rate and oxygen consumption of Donax serra was investigated to test a driving mechanism for assemblage responses to upwelling. Feeding ability was significantly reduced at colder temperatures indicating an important factor which may be involved in determining assemblage structure. These results suggest that alterations to upwelling regimes predicted under climate change scenarios will impact sandy beach macrofauna, however the specific outcome will depend on multiple contextual factors.

It is estimated that less than ten percent of the world's species have been discovered and described. The main reason for the slow pace of new species description is that the science of taxonomy, as traditionally practiced, can be very laborious: taxonomists have to manually gather and analyze data from large numbers of specimens and identify the smallest subset of external body characters that uniquely diagnoses the new species as distinct from all its known relatives. The pace of data gathering and analysis can be greatly increased by the information technology. In this paper, we propose a content-based image retrieval system for taxonomic research. The system can identify representative body shape characters of known species based on digitized landmarks and provide statistical clues for assisting taxonomists to identify new species or subspecies. The experiments on a taxonomic problem involving species of suckers in the genera Carpiodes demonstrate promising results.