Taxonomic chauvinism revisited: insight from parental care research.

PubMed

Stahlschmidt, Zachary R

2011-01-01

Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001-2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future

A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli.

PubMed

Tekin, Nilgun; Cihan, Arzu Coleri; Karaca, Basar; Cokmus, Cumhur

2017-03-30

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

EPA Science Inventory

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

PubMed Central

Häser, Annette

2016-01-01

Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

A Taxonomic Search Engine: Federating taxonomic databases using web services

PubMed Central

Page, Roderic DM

2005-01-01

Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

Taxonomical and functional microbial community selection in soybean rhizosphere

PubMed Central

Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

2014-01-01

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily

PubMed Central

2010-01-01

Background The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families. Results In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping. Conclusions The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

PubMed

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

A taxonomic review of the Neoserica (sensu lato) abnormis group (Coleoptera, Scarabaeidae, Sericini)

PubMed Central

Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

2014-01-01

Abstract The present paper revises the species belonging to the Neoserica (sensu lato) abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China), N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos), N. thailandensis sp. n. (Thailand), N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar), N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam), N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China), N. cardamomensis sp. n. (Indochina and southern China). One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included. PMID:25317056

Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

USGS Publications Warehouse

Sargos, Eric J.; Woodman, Neal; Reese, Aspen T.; Olson, Link E.

2013-01-01

Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis–T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis, T. belangeri, T. chrysogaster, and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes. We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes. T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each

Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

PubMed

Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

2012-09-01

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

PubMed

Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

2015-04-01

The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

PubMed

Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

2016-01-01

In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. Copyright © 2015 Elsevier Ltd. All rights reserved.

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

PubMed Central

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies. PMID:29270162

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis.

PubMed

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae , and P. savastanoi are later synonyms of P. amygdali and that " P. coronafaciens " should be revived as a nomenspecies.

The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

PubMed Central

Powers, T. O.; Todd, T. C.; Burnell, A. M.; Murray, P. C. B.; Fleming, C. C.; Szalanski, A. L.; Adams, B. A.; Harris, T. S.

1997-01-01

The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics. PMID:19274180

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae)

PubMed Central

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x–18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

PubMed Central

Sangster, George

2009-01-01

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’. PMID:19520805

Identifying taxonomic and functional surrogates for spring biodiversity conservation.

PubMed

Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

2018-02-27

Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

PESI - a taxonomic backbone for Europe.

PubMed

de Jong, Yde; Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D; Boegh, Phillip S; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M J C; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

PESI - a taxonomic backbone for Europe

PubMed Central

Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

Contrasting responses of functional diversity to major losses in taxonomic diversity.

PubMed

Edie, Stewart M; Jablonski, David; Valentine, James W

2018-01-23

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

2016-12-05

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Spatial distribution of citizen science casuistic observations for different taxonomic groups.

PubMed

Tiago, Patrícia; Ceia-Hasse, Ana; Marques, Tiago A; Capinha, César; Pereira, Henrique M

2017-10-16

Opportunistic citizen science databases are becoming an important way of gathering information on species distributions. These data are temporally and spatially dispersed and could have limitations regarding biases in the distribution of the observations in space and/or time. In this work, we test the influence of landscape variables in the distribution of citizen science observations for eight taxonomic groups. We use data collected through a Portuguese citizen science database (biodiversity4all.org). We use a zero-inflated negative binomial regression to model the distribution of observations as a function of a set of variables representing the landscape features plausibly influencing the spatial distribution of the records. Results suggest that the density of paths is the most important variable, having a statistically significant positive relationship with number of observations for seven of the eight taxa considered. Wetland coverage was also identified as having a significant, positive relationship, for birds, amphibians and reptiles, and mammals. Our results highlight that the distribution of species observations, in citizen science projects, is spatially biased. Higher frequency of observations is driven largely by accessibility and by the presence of water bodies. We conclude that efforts are required to increase the spatial evenness of sampling effort from volunteers.

Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria

PubMed Central

Brown-Elliott, Barbara A.; Wallace, Richard J.

2002-01-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

PubMed

Brown-Elliott, Barbara A; Wallace, Richard J

2002-10-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.

Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups.

PubMed

Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong

2016-01-01

Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs.

Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups

PubMed Central

Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong

2016-01-01

Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs. PMID:26884677

Photometric survey and taxonomic identifications of 92 near-Earth asteroids

NASA Astrophysics Data System (ADS)

Lin, Chien-Hsien; Ip, Wing-Huen; Lin, Zhong-Yi; Cheng, Yu-Chi; Lin, Hsing-Wen; Chang, Chan-Kao

2018-03-01

A photometric survey of near-Earth asteroids (NEAs) was conducted from 2012 through 2014 at Lulin Observatory, Taiwan. The measurements of the color indices, B-V, V-R, and V-I allow the classification of 92 NEAs into seven taxonomic types. Of these samples, 39 of them are new classifications. The fractional abundances of these taxonomic complexes are: A ∼3%, C∼6.5%, D∼8%, Q∼26%, S∼37%, V∼6.5%, and X∼13%. This result is similar to that of Thomas et al. (2011) even though the populations of the D- and X-complex with low albedos are under-represented. The ratio of the C-cluster to the total population of S + C clusters are 0.22 ± 0.06 for H ≤ 17.0 and 0.31 ± 0.06 for H > 17.0, indicating a slightly higher fraction of dark-object population with sizes smaller than 1 km.

Towards stressor-specific macroinvertebrate indices: Which traits and taxonomic groups are associated with vulnerable and tolerant taxa?

PubMed

Berger, Elisabeth; Haase, Peter; Schäfer, Ralf B; Sundermann, Andrea

2018-04-01

Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year <1, scrapers, aerial and aquatic active dispersal and plastron respiration. Traits associated with tolerant taxa included: adult aquatic life stages, polyvoltinism, ovoviviparity or egg clutches in vegetation, food preference for dead animals or living microinvertebrates, substrate preference for macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of

Redescription of Phalotris labiomaculatus (Serpentes, Dipsadidae, Elapomorphini), with notes on the taxonomic boundaries within the nasutus group.

PubMed

Hamdan, Breno; Da Silva, Nelson Jorge; Silva, Helder Lucio Rodrigues; Cintra, Carlos Eduardo D; De Lema, Thales

2013-01-01

Phalotris labiomaculatus Lema, 2002 was described based on a single specimen from Porto Franco, south of the Brazilian state of Maranhão, being rediscovered three years later in Mateiros, a municipality in the north of the state of Tocantins, attesting to its occurrence in the cerrado of both banks of the Tocantins River. The discovery of 28 new specimens from other localities during field expeditions (2009-2011) allowed a redescription of the species, adding new data on meristic and morpho-qualitative traits. These results enable a better diagnosis of intraspecific, ontogenetic and sexual variation, consolidating its taxonomic relationships with other species belonging to the nasutus group. The distribution map of P. labiomaculatus, as well as an identification key to the species of the natusus group, are provided. The type-locality is fixed to the municipality of Porto Franco, state of Maranhão.

Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

ERIC Educational Resources Information Center

Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

2016-01-01

Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

Community analysis of pigment patterns from 37 microalgae strains reveals new carotenoids and porphyrins characteristic of distinct strains and taxonomic groups

PubMed Central

Bérard, Jean-Baptiste; Kaas, Raymond; Pasquet, Virginie; Picot, Laurent; Cadoret, Jean-Paul

2017-01-01

Phytoplankton, with an estimated 30 000 to 1 000 000 species clustered in 12 phyla, presents a high taxonomic and ecophysiological diversity, reflected by the complex distribution of pigments among the different algal classes. High performance liquid chromatography is the gold standard method for qualitative and quantitative analysis of phytoplankton pigments in seawater and culture samples, but only a few pigments can be used as robust chemotaxonomic markers. A major challenge is thus to identify new ones, characteristic of a strain, species, class or taxon that cannot be currently identified on the basis of its pigment signature. Using an optimized extraction process coupled to a HPLC de-replication strategy, we examined the pigment composition of 37 microalgae strains, representative of the broad taxonomic diversity of marine and freshwater species (excluding cyanobacteria). For each species, the major pigments already described were unambiguously identified. We also observed the presence of several minor unidentified pigments in each chromatogram. The global analysis of pigment compositions revealed a total of 124 pigments, including 98 pigments or derivatives unidentified using the standards. Absorption spectra indicated that 35 corresponded to chlorophyll/porphyrin derivatives, 57 to carotenoids and six to derivatives having both spectral signatures. Sixty-one of these unidentified or new carotenoids and porphyrin derivatives were characteristic of particular strains or species, indicating their possible use as highly specific chemotaxonomic markers capable of identifying one strain out of the 37 selected. We developed a graphical analysis using Gephi software to give a clear representation of pigment communities among the various phytoplankton strains, and to reveal strain-characteristic and shared pigments. This made it possible to reconstruct the taxonomic evolution of microalgae classes, on the basis of the conservation, loss, and/or appearance of

Taxonomic indexing--extending the role of taxonomy.

PubMed

Patterson, David J; Remsen, David; Marino, William A; Norton, Cathy

2006-06-01

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

[Taxonomic theory for non-classical systematics].

PubMed

Pavlinov, I Ia

2012-01-01

Outlined briefly are basic principles of construing general taxonomic theory for biological systematics considered in the context of non-classical scientific paradigm. The necessity of such kind of theory is substantiated, and some key points of its elaboration are exposed: its interpretation as a framework concept for the partial taxonomic theories in various schools of systematics; elaboration of idea of cognitive situation including three interrelated components, namely subject, object, and epistemic ones; its construing as a content-wisely interpreted quasi-axiomatics, with strong structuring of its conceptual space including demarcation between axioms and inferring rules; its construing as a "conceptual pyramid" of concepts of various levels of generality; inclusion of a basic model into definition of the taxonomic system (classification) regulating its content. Two problems are indicated as fundamental: definition of taxonomic diversity as a subject domain for the systematics as a whole; definition of onto-epistemological status of taxonomic system (classification) in general and of taxa in particular.

Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici

PubMed Central

Silva-Santos, Rosane; Ramirez, Jorge L.; Galetti, Pedro M.; Freitas, Patrícia D.

2018-01-01

The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and

A Taxonomic Approach to the Gestalt Theory of Perls

ERIC Educational Resources Information Center

Raming, Henry E.; Frey, David H.

1974-01-01

This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Charting taxonomic knowledge through ontologies and ranking algorithms

NASA Astrophysics Data System (ADS)

Huber, Robert; Klump, Jens

2009-04-01

Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

A Framework for Inferring Taxonomic Class of Asteroids.

NASA Technical Reports Server (NTRS)

Dotson, J. L.; Mathias, D. L.

2017-01-01

Introduction: Taxonomic classification of asteroids based on their visible / near-infrared spectra or multi band photometry has proven to be a useful tool to infer other properties about asteroids. Meteorite analogs have been identified for several taxonomic classes, permitting detailed inference about asteroid composition. Trends have been identified between taxonomy and measured asteroid density. Thanks to NEOWise (Near-Earth-Object Wide-field Infrared Survey Explorer) and Spitzer (Spitzer Space Telescope), approximately twice as many asteroids have measured albedos than the number with taxonomic classifications. (If one only considers spectroscopically determined classifications, the ratio is greater than 40.) We present a Bayesian framework that provides probabilistic estimates of the taxonomic class of an asteroid based on its albedo. Although probabilistic estimates of taxonomic classes are not a replacement for spectroscopic or photometric determinations, they can be a useful tool for identifying objects for further study or for asteroid threat assessment models. Inputs and Framework: The framework relies upon two inputs: the expected fraction of each taxonomic class in the population and the albedo distribution of each class. Luckily, numerous authors have addressed both of these questions. For example, the taxonomic distribution by number, surface area and mass of the main belt has been estimated and a diameter limited estimate of fractional abundances of the near earth asteroid population was made. Similarly, the albedo distributions for taxonomic classes have been estimated for the combined main belt and NEA (Near Earth Asteroid) populations in different taxonomic systems and for the NEA population specifically. The framework utilizes a Bayesian inference appropriate for categorical data. The population fractions provide the prior while the albedo distributions allow calculation of the likelihood an albedo measurement is consistent with a given taxonomic

Partitioning taxonomic diversity of aquatic insect assemblages ...

EPA Pesticide Factsheets

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feeding groups (FFG) in Neotropical Savanna (southeastern Brazilian Cerrado) streams. To do so, we considered three diversity components: stream site (α), among stream sites (β1), and among hydrologic units (β2). We also evaluated the association of EPT genera composition with heterogeneity in land use, instream physical habitat structure, and instream water quality variables. The percent of EPT taxonomic α diversity (20.7%) was lower than the β1 and β2 diversities (53.1% and 26.2%, respectively). The EPT FFG α diversity (26.5%) was lower than the β1 diversity (55.8%) and higher than the β2 (17.7%) diversity. The collector-gatherer FFG was predominant and had the greatest β diversity among stream sites (β1, 55.8%). Our findings support the need for implementing regional scale conservation strategies in the Cerrado biome, which has been degraded by anthropogenic activities. Using adaptations of the US EPA’s National Aquatic Resource Survey (NARS) designs and methods, Ferreira and colleagues examined the distribution of taxonomic and functional diversity of aquatic insects among basins, stream sites within basins, and within stream sample reaches. They sampled 160 low-order stre

Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

EPA Science Inventory

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.

PubMed

Tripathi, Binu M; Moroenyane, Itumeleng; Sherman, Chen; Lee, Yoo Kyung; Adams, Jonathan M; Steinberger, Yosef

2017-07-01

The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the

Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi.

PubMed

Nilsson, R Henrik; Kristiansson, Erik; Ryberg, Martin; Larsson, Karl-Henrik

2005-07-18

During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi--a field where species identification often is prohibitively complex--and the much used ITS locus were chosen as test bed. A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service http://emerencia.math.chalmers.se, users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases

What are the taxonomic and evolutionary relationships of the Protozoa to the Protista?

PubMed

Corliss, J O

1981-01-01

In order to consider the problems of protist-protozoan interrelationships in proper perspective, a new "packaging" of phyla within the great kingdom Protista is proposed. Although it is based largely on historical groupings and is admittedly "unnatural" (nor are taxonomic names proposed for my five supraphyletic groupings), the arrangement may clarify some long-persisting problems, especially with regard to mixed algal-protozoan groups and/or phylogenies. Some three dozen phyla are recognized as comprising the kingdom, with the number that might be considered as "protozoan" ranging from 10 to 25, depending on one's viewpoint. No taxon should have the formal name "Protozoa", "Phytoflagellate" and "zooflagellate" are also misleading categories. Taxonomic and evolutionary relationships of phyla containing protozoa (with small "p") are inextricably intermeshed with those of other protist phyla, and thus no unified protozoan super-group exists.

A Falsification of the Citation Impediment in the Taxonomic Literature

PubMed Central

Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

2015-01-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could

Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species.

PubMed

Borges, Paulo A V; Amorim, Isabel R; Terzopoulou, Sofia; Rigal, François; Emerson, Brent C; Serrano, Artur R M

2017-02-23

Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level. A total of four new species are described grouped into two complexes: i) two new species in the "complex tornvalli" with the new taxa Tarphius relictus sp. nov. (Terceira) and Tarphius furtadoi sp. nov. (São Jorge, Faial and Pico) and; ii) two new species in the "complex azoricus-wollastoni-depressus" with the new taxa Tarphius gabrielae sp. nov. (Pico) and Tarphius floresensis sp. nov. (Flores). Descriptions, photographs of holotypes and morphological details, and remarks on diagnostic features comparing similar species are presented. Additional information on the distribution and conservation status of the 12 described species in the archipelago is also provided.

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Methé, Barbara A.

2013-01-01

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat’s microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of “minor” oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region. PMID

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

PubMed

Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

2006-12-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

USGS Publications Warehouse

Beever, E.A.; Haig, S.M.; Chambers, Steven M.; Draheim, Hope M.; Dugger, Bruce D.; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B.; Kesler, Dylan C.; Knaus, Brian J.; Lopes, Iara F.; Loschl, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

2006-01-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Complex depth-related patterns in taxonomic and functional diversity of polychaetes in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Carvalho, Russell; Wei, Chih-Lin; Rowe, Gilbert; Schulze, Anja

2013-10-01

Patterns of taxonomic and functional diversity in polychaete assemblages were examined in the deep northern Gulf of Mexico, including the first analysis of polychaete feeding guild distribution. An analysis of samples from a total of 51 stations located along 7 transects plus additional nearby sites, indicated that density decreased exponentially with depth, with the central locations having higher densities than the eastern and western regions. Alpha diversity was also highest at the central stations associated with the Mississippi trough. The samples can be grouped into three significant clusters based on thirty percent similarity of species composition. BIO-ENV indicated depth, sediment particle size, and export POC were most important variables explaining distributions. The diversity of polychaete feeding guilds was high in the Mississippi trough, upper and mid-slope regions but declined to a few guilds on the Sigsbee abyssal plain. Combining feeding guild analysis with traditional analysis of species diversity contributes to a clearer understanding of trophic diversity in deep-sea benthic assemblages.

Adding complexity to the complex: new insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae).

PubMed

Fernández, Rosa; Almodóvar, Ana; Novo, Marta; Simancas, Bárbara; Díaz Cosín, Darío J

2012-08-01

The importance of the Aporrectodea caliginosa species complex lies in the great abundance and wide distribution of the species which exist within it. For more than a century, chaos has surrounded this complex; morphological criteria has failed to solve the taxonomic status of these species. This present body of work aims to study the phylogeny of this complex by increasing the number of samples used in previous molecular works and by including morphologically-similar species that were never studied using molecular tools (A. giardi, Nicodrilus monticola, N. carochensis and N. tetramammalis). Two basal clades were obtained: one formed by A. caliginosa and A. tuberculata and the other by the rest of the species. This second clade was divided into two more: one with Eurosiberian and another with Mediterranean forms. A. caliginosa and A. longa were divided into two paraphyletic groups. Both A. giardi and A. nocturna showed characteristics consistent with monophyletic groups. Each of the two recovered lineages of A. trapezoides were phylogenetically related to different sexual species. While lineage I of A. trapezoides was monophyletic, lineage II resulted to be paraphyletic, as well as the three Nicodrilus 'species'. The diversification of the complex occurred during the Late Miocene-Early Pliocene (6.92-11.09 Mya). The parthenogenetic forms within the Mediterranean clade would have diversified before the ones in the Eurosiberian clade (3.13-4.64 Mya and 1.05-3.48 Mya, respectively), thus implying the existence not only of at least two different moments in which parthenogenesis arose within this complex of species, but also of two different and independent evolutionary lines. Neither the 4× rule nor the GMYC method for species delimitation were successful for distinguishing taxonomically-distinct species. Copyright © 2012 Elsevier Inc. All rights reserved.

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Erika C.; Gido, Keith B.; Bello, Nora

Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

DOE PAGES

Martin, Erika C.; Gido, Keith B.; Bello, Nora; ...

2016-04-06

Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources

A Falsification of the Citation Impediment in the Taxonomic Literature.

PubMed

Steiner, Florian M; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C

2015-09-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009-2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could

Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

PubMed Central

Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

2012-01-01

The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

NASA Astrophysics Data System (ADS)

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

PubMed

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Control of complex physically simulated robot groups

NASA Astrophysics Data System (ADS)

Brogan, David C.

2001-10-01

Actuated systems such as robots take many forms and sizes but each requires solving the difficult task of utilizing available control inputs to accomplish desired system performance. Coordinated groups of robots provide the opportunity to accomplish more complex tasks, to adapt to changing environmental conditions, and to survive individual failures. Similarly, groups of simulated robots, represented as graphical characters, can test the design of experimental scenarios and provide autonomous interactive counterparts for video games. The complexity of writing control algorithms for these groups currently hinders their use. A combination of biologically inspired heuristics, search strategies, and optimization techniques serve to reduce the complexity of controlling these real and simulated characters and to provide computationally feasible solutions.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PubMed Central

Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.

PubMed

Dos Santos, E F; Noll, F B; Brandão, C R F

2014-04-01

Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters.

A taxonomic wish-list for community ecology.

PubMed Central

Gotelli, Nicholas J

2004-01-01

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

Global Taxonomic Diversity of Living Reptiles

PubMed Central

Pincheira-Donoso, Daniel; Bauer, Aaron M.; Meiri, Shai; Uetz, Peter

2013-01-01

Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world’s diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

Global taxonomic diversity of living reptiles.

PubMed

Pincheira-Donoso, Daniel; Bauer, Aaron M; Meiri, Shai; Uetz, Peter

2013-01-01

Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

ERIC Educational Resources Information Center

Whitmore, Jeannette M.; Shore, Wendelyn J.; Smith, Peg Hull

2004-01-01

The type of information (taxonomic or thematic) available at different levels of knowledge was investigated. Following extensive norming to identify taxonomic and thematic associates of low-frequency nouns, participants determined if taxonomic or thematic associates were meaningfully related to target words at three levels of knowledge: target…

Polyether complexes of groups 13 and 14.

PubMed

Swidan, Ala'aeddeen; Macdonald, Charles L B

2016-07-21

Notable aspects of the chemistry of complexes of polyether ligands including crown ethers, cryptands, glycols, glymes, and related polyether ligands with heavier group 13 and 14 elements are reviewed with a focus on results from 2005 to the present. The majority of reported polyether complexes contain lead(ii) and thallium(i) but recent breakthroughs in regard to the preparation of low oxidation state reagents of the lighter congeners have allowed for the generation of complexes containing indium(i), gallium(i), germanium(ii), and even silicon(ii). The important roles of ligand size, donor types, and counter anions in regard to the chemical properties of the polyether complexes is highlighted. A particular focus on the structural aspects of the numerous coordination complexes provides a rationale for some of the spectacular contributions that such compounds have made to Modern Main Group Chemistry.

Taxonomic turmoil down-under: recent developments in Australian orchid systematics

PubMed Central

Hopper, Stephen D.

2009-01-01

Background The issue of determining the most appropriate rank for each accepted taxon fuels ongoing controversy throughout systematics. The particularly marked escalation of such issues in modern Australian orchid systematics merits examination, not only because of wider implications in taxonomy but also because of direct effects on studies of comparative biology and conservation management. Scope This paper briefly reviews the causes of recent taxonomic turmoil for Australian orchids and outlines new research opportunities and conservation implications arising from an improved understanding of their molecular phylogenetics. Conclusions DNA sequencing and intensified field work have contributed towards a much improved understanding of Australian orchid systematics. Great progress has been made in discerning monophyletic groups or clades. Fresh interpretations of morphological evolution have been made possible by comparisons with the results of DNA analyses. Significant conceptual shifts from polymorphic species concepts to biological and phylogenetic concepts have also elevated the discovery and description of new species. Consequently, over the past decade, the number of Australian orchid species recognized by taxonomists has risen from approx. 900 to 1200. Similarly, the number of genera recognized by some taxonomists has increased from 110 to 192, resulting in 45% of Australian species/subspecies being assigned a new generic epithet since 2000. At higher taxonomic levels, much of the recent controversy in Australian orchid systematics reflects a divergence in views about where to split and assign formal names within unequivocally monophyletic groups. Differences regarding typification in the case of Caladenia have added additional confusion and complexity. However, new insights into and research opportunities concerning speciation processes in orchids have arisen from the wealth of new data and discrimination of species. Robustly supported molecular analyses of

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

PubMed Central

Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

PubMed

Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area.

Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts

PubMed Central

Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

2018-01-01

Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems. PMID

Multi-Dimensional Scaling based grouping of known complexes and intelligent protein complex detection.

PubMed

Rehman, Zia Ur; Idris, Adnan; Khan, Asifullah

2018-06-01

Protein-Protein Interactions (PPI) play a vital role in cellular processes and are formed because of thousands of interactions among proteins. Advancements in proteomics technologies have resulted in huge PPI datasets that need to be systematically analyzed. Protein complexes are the locally dense regions in PPI networks, which extend important role in metabolic pathways and gene regulation. In this work, a novel two-phase protein complex detection and grouping mechanism is proposed. In the first phase, topological and biological features are extracted for each complex, and prediction performance is investigated using Bagging based Ensemble classifier (PCD-BEns). Performance evaluation through cross validation shows improvement in comparison to CDIP, MCode, CFinder and PLSMC methods Second phase employs Multi-Dimensional Scaling (MDS) for the grouping of known complexes by exploring inter complex relations. It is experimentally observed that the combination of topological and biological features in the proposed approach has greatly enhanced prediction performance for protein complex detection, which may help to understand various biological processes, whereas application of MDS based exploration may assist in grouping potentially similar complexes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Taxonomic and Thematic Semantic Systems

PubMed Central

Mirman, Daniel; Landrigan, Jon-Frederick; Britt, Allison E.

2017-01-01

Object concepts are critical for nearly all aspects of human cognition, from perception tasks like object recognition, to understanding and producing language, to making meaningful actions. Concepts can have two very different kinds of relations: similarity relations based on shared features (e.g., dog – bear), which are called “taxonomic” relations, and contiguity relations based on co-occurrence in events or scenarios (e.g., dog – leash), which are called “thematic” relations. Here we report a systematic review of experimental psychology and cognitive neuroscience evidence of this distinction in the structure of semantic memory. We propose two principles that may drive the development of distinct taxonomic and thematic semantic systems: (1) differences between which features determine taxonomic vs. thematic relations and (2) differences in the processing required to extract taxonomic vs. thematic relations. This review brings together distinct threads of behavioral, computational, and neuroscience research on semantic memory in support of a functional and neural dissociation, and defines a framework for future studies of semantic memory. PMID:28333494

Benthic impacts of intertidal oyster culture, with consideration of taxonomic sufficiency.

PubMed

Forrest, Barrie M; Creese, Robert G

2006-01-01

An investigation of the impacts from elevated intertidal Pacific oyster culture in a New Zealand estuary showed enhanced sedimentation beneath culture racks compared with other sites. Seabed elevation beneath racks was generally lower than between them, suggesting that topographic patterns more likely result from a local effect of rack structures on hydrodynamic processes than from enhanced deposition. Compared with control sites, seabed sediments within the farm had a greater silt/clay and organic content, and a lower redox potential and shear strength. While a marked trend in macrofaunal species richness was not evident, species composition and dominance patterns were consistent with a disturbance gradient, with farm effects not evident 35 m from the perimeter of the racks. Of the environmental variables measured, sediment shear strength was most closely associated with the distribution and density of macrofauna, suggesting that human-induced disturbance from farming operations may have contributed to the biological patterns. To evaluate the taxonomic sufficiency needed to document impacts, aggregation to the family level based on Linnean classification was compared with an aggregation scheme based on ;general groups' identifiable with limited taxonomic expertise. Compared with species-level analyses, spatial patterns of impact were equally discernible at both aggregation levels used, provided density rather than presence/absence data were used. Once baseline conditions are established and the efficacy of taxonomic aggregation demonstrated, a ;general group' scheme provides an appropriate and increasingly relevant tool for routine monitoring.

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative.

PubMed

Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J; Loader, Simon P; Simon, Chris; Nagel, Peter

2016-01-01

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a "complex within the complex": the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

PubMed Central

Spring, Stefan; Scheuner, Carmen; Göker, Markus; Klenk, Hans-Peter

2015-01-01

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov. PMID:25914684

Insights from Zootaxa on potential trends in zoological taxonomic activity

PubMed Central

2011-01-01

Background An opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed. Discussion We found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species". Summary The taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not. PMID:21418568

The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.

PubMed

Cho, Yong-Joon; Yi, Hana; Chun, Jongsik; Cho, Sang-Nae; Daley, Charles L; Koh, Won-Jung; Shin, Sung Jae

2013-01-01

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dees, C.; Ringleberg, D.; Scott, T.C.

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescensmore » with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.« less

Current Taxonomical Situation of Streptococcus suis

PubMed Central

Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

2016-01-01

Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several “S. suis-like strains” that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains. PMID:27348006

Current Taxonomical Situation of Streptococcus suis.

PubMed

Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

2016-06-24

Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several "S. suis-like strains" that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains.

Taxonomic bias in biodiversity data and societal preferences.

PubMed

Troudet, Julien; Grandcolas, Philippe; Blin, Amandine; Vignes-Lebbe, Régine; Legendre, Frédéric

2017-08-22

Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Seasonality, Dietary Overlap and the Role of Taxonomic Resolution in the Study of the Diet of Three Congeneric Fishes from a Tropical Bay

PubMed Central

Pombo, Maíra; Denadai, Márcia Regina; Turra, Alexander

2013-01-01

Not only seasonality but also taxonomic resolution of prey categories has been shown to affect diet studies. We analyzed the stomach contents of three sympatric species, Stellifer rastrifer, S. brasiliensis and S. stellifer, sampled monthly from August 2003 to October 2004 in Caraguatatuba Bay, southeastern Brazil. General characteristics and similarities among their diets were evaluated by considering high taxonomic ranks of all prey groups, and also the lower taxonomic ranks of the main prey groups. Dietary similarity was relatively high among species and low between seasons, and both evaluation criteria gave the equivalent results. The rare items, however, provided information about resource partition, and the species compositions of the most important groups were apparently good indicators of food availability. PMID:23405256

Plastome data reveal multiple geographic origins of Quercus Group Ilex

PubMed Central

Grimm, Guido W.; Papini, Alessio; Vessella, Federico; Cardoni, Simone; Tordoni, Enrico; Piredda, Roberta; Franc, Alain; Denk, Thomas

2016-01-01

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not

How complex is the Bufo bufo species group?

PubMed

Arntzen, Jan W; Recuero, Ernesto; Canestrelli, Daniele; Martínez-Solano, Iñigo

2013-12-01

Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and García-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that García-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Resolving cryptic species complexes of major tephritid pests

PubMed Central

Hendrichs, Jorge; Vera, M. Teresa; De Meyer, Marc; Clarke, Anthony R.

2015-01-01

Abstract An FAO/IAEA Co-ordinated Research Project (CRP) on “Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade” was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex – Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex – Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, Bactrocera papayae, Bactrocera philippinensis and Bactrocera invadens, the latter three species were synonymized with Bactrocera dorsalis. Of the five target pest taxa studied, only Bactrocera dorsalis and Bactrocera carambolae remain as

Bacterial and Phytoplankton Responses to Nutrient Amendments in a Boreal Lake Differ According to Season and to Taxonomic Resolution

PubMed Central

Peura, Sari; Eiler, Alexander; Hiltunen, Minna; Nykänen, Hannu; Tiirola, Marja; Jones, Roger I.

2012-01-01

Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions. PMID:22715392

A taxonomic review of the Selenophori group (Coleoptera, Carabidae, Harpalini) in the West Indies, with descriptions of new species and notes about classification and biogeography

PubMed Central

Shpeley, Danny; Hunting, Wesley; Ball, George E.

2017-01-01

Abstract Primarily a taxonomic review of the West Indian elements of the selenophorine Harpalini, this paper includes a classification, a key, descriptions and illustrations of taxa, re-rankings, and new synonymies. In total, 45 species and subspecies are treated, six of which are described as new. A new genus and new species are as follows, with type localities in parentheses: Paraulacoryssus gen. n., (type species Selenophorus puertoricensis Mutchler, 1934); Neodiachipteryx davidsoni sp. n., (Zamba, Dominican Republic); Selenophorus spinosus sp. n., seriatoporus species group (Benjamin Constant, state of Amazonas, Brazil); Selenophorus obtusoides sp. n., parumpunctatus species group (near Soroa, Pinar del Rio Province, Cuba); Selenophorus iviei sp. n., nonseriatus species group (Big River, Montserrat, 16°45.719N', 62°11.335W'); Selenophorus irec sp. n., nonseriatus species group (Vernou, Guadeloupe, Lesser Antilles); and Selenophorus fabricii sp. n., opalinus species group (Cabo Rojo, Pedernales Province, Dominican Republic). This last species was misidentified as Selenophorus integer (Fabricius). In turn, that species was misidentified as Selenophorus chalybeus Dejean. Selenophorus chalybeus Dejean is a junior synonym of Selenophorus integer Fabricius, syn. n.; and Isopleurus macleayi Kirby is a junior synonym of Selenophorus pyritosus Dejean, syn. n. Biogeographically, log of land area plotted against log of number of species shows that the equilibrium theory of biogeography applies to the West Indian selenophorine fauna. Taxonomically, the selenophorine taxa of the West Indies are arranged in eight genera. The 30 species/subspecies of Selenophorus (sensu stricto) are arranged in 10 species groups. Geographically, the major sources of the selenophorines are the Bahamas, the Greater Antilles and Lesser Antilles. The West Indian islands probably have been invaded by 26 taxa. Of the currently extant taxa, 11 are classified as immigrant, meaning that they are

A taxonomic review of the Selenophori group (Coleoptera, Carabidae, Harpalini) in the West Indies, with descriptions of new species and notes about classification and biogeography.

PubMed

Shpeley, Danny; Hunting, Wesley; Ball, George E

2017-01-01

Primarily a taxonomic review of the West Indian elements of the selenophorine Harpalini, this paper includes a classification, a key, descriptions and illustrations of taxa, re-rankings, and new synonymies. In total, 45 species and subspecies are treated, six of which are described as new. A new genus and new species are as follows, with type localities in parentheses: Paraulacoryssus gen. n. , (type species Selenophorus puertoricensis Mutchler, 1934); Neodiachipteryx davidsoni sp. n. , (Zamba, Dominican Republic); Selenophorus spinosus sp. n. , seriatoporus species group (Benjamin Constant, state of Amazonas, Brazil); Selenophorus obtusoides sp. n. , parumpunctatus species group (near Soroa, Pinar del Rio Province, Cuba); Selenophorus iviei sp. n. , nonseriatus species group (Big River, Montserrat, 16°45.719N', 62°11.335W'); Selenophorus irec sp. n. , nonseriatus species group (Vernou, Guadeloupe, Lesser Antilles); and Selenophorus fabricii sp. n. , opalinus species group (Cabo Rojo, Pedernales Province, Dominican Republic). This last species was misidentified as Selenophorus integer (Fabricius). In turn, that species was misidentified as Selenophorus chalybeus Dejean. Selenophorus chalybeus Dejean is a junior synonym of Selenophorus integer Fabricius, syn. n. ; and Isopleurus macleayi Kirby is a junior synonym of Selenophorus pyritosus Dejean, syn. n. Biogeographically, log of land area plotted against log of number of species shows that the equilibrium theory of biogeography applies to the West Indian selenophorine fauna. Taxonomically, the selenophorine taxa of the West Indies are arranged in eight genera. The 30 species/subspecies of Selenophorus ( sensu stricto ) are arranged in 10 species groups. Geographically, the major sources of the selenophorines are the Bahamas, the Greater Antilles and Lesser Antilles. The West Indian islands probably have been invaded by 26 taxa. Of the currently extant taxa, 11 are classified as immigrant , meaning that they are

Hitting the right target: taxonomic challenges for, and of, plant invasions

PubMed Central

Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

2013-01-01

This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

Distinct progression of the deterioration of thematic and taxonomic links in natural and manufactured objects in Alzheimer's disease.

PubMed

Simoes Loureiro, Isabelle; Lefebvre, Laurent

2016-10-01

Taxonomic and thematic relationships are core elements of lexico-semantic networks. However, the weight of both links differs in semantic memory, with distinct support for natural and manufactured objects: natural objects tend to be more taxonomically identified while manufactured objects benefit more from the underlying thematic relationships. Alzheimer's disease (AD) causes early semantic memory impairment characterized by a category-specific deterioration, where natural objects are more sensitive to the disease than manufactured objects. However, relatively few studies have examined the progressive deterioration of specific thematic versus taxonomic relations in both categories of objects in AD. To better understand semantic memory disorganization in AD and analyze the potential interaction effect between the category (natural/manufactured), the condition (thematic/taxonomic) and AD, we will investigate the lexico-semantic network in 82 AD patients (divided into three groups depending on their global cognitive deterioration and their performance in a preliminary semantic knowledge questionnaire (mild (AD1), moderate (AD2) and advanced (AD3) stages of semantic knowledge alteration). The experimental protocol contains two tasks: an implicit semantic priming paradigm and an explicit card-sorting test that uses the same items, equally divided between natural and manufactured objects. Results show a distinct taxonomic and thematic evolution pattern with early taxonomic deterioration. Natural objects are also more vulnerable to the disease. Lastly, there is an interaction effect between the category and the condition in the priming task indicating that natural objects are more taxonomically organized and manufactured objects benefit more from both thematic and taxonomic organizations, reinforcing the idea of the robustness of this category. The theoretical accounts of these observations will be discussed in detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of Xiphinema americanum group species (Nematoda: Dorylaimida) and co-evolution of bacteria from the genus ‘Candidatus Xiphinematobacter’ with these nematodes

USDA-ARS?s Scientific Manuscript database

The Xiphinema americanum group contains over two-dozen different species of nematode. They are economically important because they vector nepoviruses, which cause damage to several crops. Taxonomic differentiation among species of the X. americanum complex is problematic because many of the species ...

Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

PubMed Central

Anu, Anto; Sabu, Thomas K.

2007-01-01

The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

The taxonomic status of genetically divergent populations of Lutzomyia longipalpis (Diptera: Psychodidae) based on the distribution of mitochondrial and isozyme variation.

PubMed

Arrivillaga, Jazzmin; Mutebi, John-Paul; Piñango, Hermes; Norris, Douglas; Alexander, Bruce; Feliciangeli, M Dora; Lanzaro, Gregory C

2003-09-01

The sand fly, Lutzomyia longipalpis (Lutz & Neiva) reputedly is a complex of cryptic species; however, there is currently no consensus as to the number of species in the complex or their geographic distributions. We conducted phylogenetic analyses of 31 populations from throughout the species range, using seven isozyme loci and genes in the mitochondrial genome. Analyses of these two independent sets of markers were largely concordant and revealed four distinct clades that support the existence of four species. The four clades have distinct geographic ranges: (1) Brazil (Species A = Lu. longipalpis sensu stricto), (2) Laran (Species B = Lu. pseudolongipalpis), (3) cis-Andean (Species C), and (4) trans-Andean (Species D). The cis-Andean clade may be subdivided further into two groups, one in Colombia and one in northwestern Venezuela, but their taxonomic status remains unresolved. Knowledge that Lu. longipalpis is a complex of species may ultimately shed light on anomalies in the epidemiology of visceral leishmaniasis in the New World.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

PubMed

Savic, Olivera; Savic, Andrej M; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials

PubMed Central

Savic, Olivera; Savic, Andrej M.; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280–460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520–600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation. PMID:29236767

Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

PubMed Central

Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

2017-01-01

Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features

PubMed Central

Wuyts, Sander; Wittouck, Stijn; De Boeck, Ilke; Allonsius, Camille N.; Pasolli, Edoardo

2017-01-01

ABSTRACT Although the genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a Lactobacillus strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains. This led to the identification of a catalase-encoding gene in all 10 L. casei sensu stricto strains, making it the first described catalase-positive species in the Lactobacillus genus. Moreover, we found that 6 of 10 L. casei genomes contained a SecA2/SecY2 gene cluster with two putative glycosylated surface adhesin proteins. Altogether, our results highlight current inconsistencies in the taxonomy of the L. casei group and reveal new clade-associated functional features. IMPORTANCE The closely related species of the Lactobacillus casei group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the L. casei species. We find that after reclassification, only 10 genomes remain classified as L. casei. These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an L. casei strain from the human upper respiratory tract and discovered that it and multiple other L. casei strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae)

PubMed Central

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G.

2018-01-01

Abstract Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised. PMID:29416412

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

PubMed

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

2018-01-01

Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera , which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

Systematic and biogeographic review of the Staphylinini rove beetles of Lord Howe Island with description of new species and taxonomic changes (Coleoptera, Staphylinidae)

PubMed Central

Shaw, Josh Jenkins; Solodovnikov, Alexey

2016-01-01

Abstract Lord Howe is an oceanic and relatively young island situated in an area of complex geological and therefore biogeographical processes. The island boasts a large number of endemic species, including many beetles, however, few groups are in an adequate state of systematic knowledge for biogeographic investigation. Recent advances in the systematics of the hyper-diverse rove beetle tribe Staphylinini on a global scale enable us to implement taxonomic changes for species from Lord Howe Island. With the improved systematics we are able to make more accurate biogeographic conclusions and set a framework for further more in-depth exploration of this unique island using rove beetles. Two new species are described: Cheilocolpus olliffi sp. n. and Quediopsis howensis sp. n. Taxonomic changes for the tribe are implemented resulting in the following new combinations: Cheilocolpus castaneus (Lea, 1925), comb. n., Cheilocolpus kentiae (Lea, 1925), comb. n., Ctenandropus mirus (Lea, 1925), comb. n., and Hesperus dolichoderes (Lea, 1925), comb. n. With the updated state of knowledge, the Staphylinini fauna of Lord Howe Island appears to be mainly derived from lineages on mainland Australia. PMID:28174494

A taxonomic revision of Herminium L. (Orchidoideae, Orchidaceae)

PubMed Central

Raskoti, Bhakta Bahadur; Schuiteman, André; Jin, Wei-Tao; Jin, Xiao-Hua

2017-01-01

Abstract Herminium (Orchidaceae, Orchidoideae) is a medium-sized genus widespread in the northern hemisphere, with a clear centre of diversity in the Himalayas. We present a comprehensive taxonomic revision of Herminium based on field observations and morphological studies, for which we examined about 2500 specimens. We recognize 49 species grouped into six formal sections, including one new species, Herminium tibeticum, from Tibet. We provide an identification key to the species, descriptions of the species, notes on ecology and distribution, and complete nomenclature for each species, including typifications. We here designate lectotypes for five species and reduce four taxa to synonymy. PMID:28794677

Designing Multimedia Games for Young Children's Taxonomic Concept Development

ERIC Educational Resources Information Center

Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

2008-01-01

This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

Preschool Children's Taxonomic Knowledge of Animal Species

ERIC Educational Resources Information Center

Allen, Michael

2015-01-01

Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

Infrared multiple photon dissociation spectroscopy of group I and group II metal complexes with Boc-hydroxylamine.

PubMed

Dain, Ryan P; Gresham, Gary; Groenewold, Gary S; Steill, Jeffrey D; Oomens, Jos; Van Stipdonk, Michael J

2013-08-30

Hydroxamates are essential growth factors for some microbes, acting primarily as siderophores that solubilize iron for transport into a cell. Here we determined the intrinsic structure of 1:1 complexes between Boc-protected hydroxylamine and group I ([M(L)](+)) and group II ([M(L-H)](+)) cations, where M and L are the cation and ligand, respectively, which are convenient models for the functional unit of hydroxamate siderphores. The relevant complex ions were generated by electrospray ionization (ESI) and isolated and stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Infrared spectra of the isolated complexes were collected by monitoring (infrared) photodissociation yield as a function of photon energy. Experimental spectra were then compared to those predicted by density functional theory (DFT) calculations. The infrared multiple photon dissociation (IRMPD) spectra collected are in good agreement with those predicted to be lowest-energy by DFT. The spectra for the group I complexes contain six resolved absorptions that can be attributed to amide I and II type and hydroxylamine N-OH vibrations. Similar absorptions are observed for the group II cation complexes, with shifts of the amide I and amide II vibrations due to the change in structure with deprotonation of the hydroxylamine group. IRMPD spectroscopy unequivocally shows that the intrinsic binding mode for the group I cations involves the O atoms of the amide carbonyl and hydroxylamine groups of Boc-hydroxylamine. A similar binding mode is preferred for the group II cations, except that in this case the metal ion is coordinated by the O atom of the deprotonated hydroxylamine group. Copyright © 2013 John Wiley & Sons, Ltd.

Geographical and taxonomic biases in invasion ecology.

PubMed

Pysek, Petr; Richardson, David M; Pergl, Jan; Jarosík, Vojtech; Sixtová, Zuzana; Weber, Ewald

2008-05-01

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.

Macrozooplankton biomass in a warm-core Gulf Stream ring: Time series changes in size structure, taxonomic composition, and vertical distribution

NASA Astrophysics Data System (ADS)

Davis, Cabell S.; Wiebe, Peter H.

1985-01-01

Macrozooplankton size structure and taxonomic composition in warm-core ring 82B was examined from a time series (March, April, June) of ring center MOCNESS (1 m) samples. Size distributions of 15 major taxonomic groups were determined from length measurements digitized from silhouette photographs of the samples. Silhouette digitization allows rapid quantification of Zooplankton size structure and taxonomic composition. Length/weight regressions, determined for each taxon, were used to partition the biomass (displacement volumes) of each sample among the major taxonomic groups. Zooplankton taxonomic composition and size structure varied with depth and appeared to coincide with the hydrographic structure of the ring. In March and April, within the thermostad region of the ring, smaller herbivorous/omnivorous Zooplankton, including copepods, crustacean larvae, and euphausiids, were dominant, whereas below this region, larger carnivores, such as medusae, ctenophores, fish, and decapods, dominated. Copepods were generally dominant in most samples above 500 m. Total macrozooplankton abundance and biomass increased between March and April, primarily because of increases in herbivorous taxa, including copepods, crustacean larvae, and larvaceans. A marked increase in total macrozooplankton abundance and biomass between April and June was characterized by an equally dramatic shift from smaller herbivores (1.0-3.0 mm) in April to large herbivores (5.0-6.0 mm) and carnivores (>15 mm) in June. Species identifications made directly from the samples suggest that changes in trophic structure resulted from seeding type immigration and subsequent in situ population growth of Slope Water zooplankton species.

Not so sluggish: the success of the Felimare picta complex (Gastropoda, Nudibranchia) crossing Atlantic biogeographic barriers

PubMed Central

Levy, André

2016-01-01

The molecular phylogeny of the Atlanto-Mediterranean species of the genus Felimare, particularly those attributed to the species F. picta, was inferred using two mitochondrial markers (16S and COI). A recent revision of the Chromodorididae clarified the taxonomic relationships at the family level redefining the genus Felimare. However, conflicting taxonomic classifications have been proposed for a restrict group of taxa with overlapping morphological characteristics and geographical distributions designated here as the Felimare picta complex. Three major groups were identified: one Mediterranean and amphi-Atlantic group; a western Atlantic group and a tropical eastern Atlantic group. F. picta forms a paraphyletic group since some subspecies are more closely related with taxa traditionaly classified as independent species (e.g. F. zebra) than with other subspecies with allopatric distributions (e.g. F. picta picta and F. picta tema). Usually, nudibranchs have adhesive demersal eggs, short planktonic larval phases and low mobility as adults unless rafting on floating materials occurs. Surprisingly however, the phylogeny of the F. picta complex suggests that they successfully cross main Atlantic biogeographic barriers including the mid-Atlantic barrier. This ability to cross different biogeographic barriers may be related to F. picta’s distinct life history and ecological traits. Compared to other Chromodorididae F. picta has larger eggs and planktotrophic larvae which could be related to a longer planktonic phase. PMID:26823995

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

PubMed Central

Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J.; Loader, Simon P.; Simon, Chris; Nagel, Peter

2016-01-01

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

The Neural Bases of Taxonomic and Thematic Conceptual Relations: An MEG Study

PubMed Central

Lewis, Gwyneth A.; Poeppel, David; Murphy, Gregory L.

2015-01-01

Converging evidence from behavioral and neuroimaging studies of human concepts indicate distinct neural systems for taxonomic and thematic knowledge. A recent study of naming in aphasia found involvement of the anterior temporal lobe (ATL) during taxonomic (feature-based) processing, and involvement of the temporoparietal junction (TPJ) during thematic (function-based) processing. We conducted an online magnetoencephalography (MEG) study to examine the spatio-temporal nature of taxonomic and thematic relations. We measured participants’ brain responses to words preceded by either a taxonomically or thematically related item (e.g., cottage→castle, king→castle). In a separate experiment we collected relatedness ratings of the word pairs from participants. We examined effects of relatedness and relation type on activation in ATL and TPJ regions of interest (ROIs) using permutation t-tests to identify differences in ROI activation between conditions as well as single-trial correlational analyses to examine the millisecond-by-millisecond influence of the stimulus variables on the ROIs. Taxonomic relations strongly predicted ATL activation, and both kinds of relations influenced the TPJ. Our results further strengthen the view of the ATL's importance to taxonomic knowledge. Moreover, they provide a nuanced view of thematic relations as involving taxonomic knowledge. PMID:25582406

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

PubMed

Hamedi, Javad; Mohammadipanah, Fatemeh

2015-02-01

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Taxonomic history and invasion biology of two Phyllonorycter leaf miners (Lepidoptera: Gracillariidae) with links to taxonomic and molecular datasets.

PubMed

De Prins, Jurate; De Prins, Willy; De Coninck, Eliane; Kawahara, Akito Y; Milton, Megan A; Hebert, Paul D N

2013-01-01

This paper deals with two European species, Phyllonorycter mespilella (Hübner, 1805) and P. trifasciella (Haworth, 1828), that have colonized the subtropical Canary Islands. The Rosaceae leaf miner, P. mespilella, is recorded for the first time from Lanzarote and La Palma, while the Caprifoliaceae leaf miner, P. trifasciella, is recorded from Tenerife. We present the diagnoses of these species based on morphology, a preliminary DNA barcode (COI) library of congeneric and con-familial species, and discuss the taxonomic position of the colonizers within the blancardella and trifasciella species groups. The recent intensification of anthropogenic disturbance likely accounts for their range expansion, an event that may impact the relict flora present on the Canary Islands.

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

PubMed

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

Individual differences in the strength of taxonomic versus thematic relations

PubMed Central

Mirman, Daniel; Graziano, Kristen M.

2011-01-01

Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) based on shared features, or thematically (eating breakfast, taking a dog for a walk, etc.) based on participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a single spoken word, even when the listener is not required to perform any active task. The results further revealed that an individual’s relative activation of taxonomic relations compared to thematic relations predicts that individual’s tendency to favor taxonomic over thematic relations when asked to choose between them in a similarity judgment task. These results argue that individuals differ in the relative strengths of their taxonomic and thematic semantic knowledge and suggest that meaning information is organized in two parallel, complementary semantic systems. PMID:22201413

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae).

PubMed

Mishra, Priyanka; Kumar, Amit; Rodrigues, Vereena; Shukla, Ashutosh K; Sundaresan, Velusamy

2016-01-01

-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain

PubMed Central

Schwartz, Myrna F.; Kimberg, Daniel Y.; Walker, Grant M.; Brecher, Adelyn; Faseyitan, Olufunsho K.; Dell, Gary S.; Mirman, Daniel; Coslett, H. Branch

2011-01-01

It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain. PMID:21540329

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

The Macrobiotus hufelandi group (Tardigrada) revisited.

PubMed

Kaczmarek, Łukasz; Michalczyk, Łukasz

2017-12-08

Species of the Macrobiotus hufelandi group are one of the most often recorded tardigrades throughout the globe. For over a century M. hufelandi has been considered cosmopolitan but in recent decades numerous species of similar morphologies have been described from various continents, which suggests that what was originally defined as a single taxon is, in fact, a complex of species. The definition of the hufelandi group is subject to a long-standing discussion and in this paper we propose a refined set of characters that are hoped to elucidate the taxonomic status of the group. In order to aid interspecific comparisons, we also propose a unified nomenclature for the crucial morphological traits and clar.

Taxonomic revision of the species of Parvanachis Radwin, 1968 (Gastropoda: Columbellidae) from the Gulf of Panama.

PubMed

de Maintenon, Marta J

2014-01-07

Species of Parvanachis Radwin, 1968 collected from the Gulf of Panama are anatomically characterized and taxonomically revised. Six species are reported to occur in the region: P. pygmaea (Sowerby, 1832), P. pardalis (Hinds, 1843), P. diminuta (C.B. Adams, 1852), P. albonodosa (Carpenter, 1857), P. milium (Dall, 1916), and P. dalli Bartsch, 1931. Of these six, three are confirmed as described. P. milium was not found in new collections or the previous survey collection and may be more common further south. P. dalli is a synonym of P. pygmaea; and P. albonodosa (auct.) is renamed, because the type material represents a different species. Two new species are described, P. dichroma and P. adamsi. P. pardalis, based on anatomy and shell and radular morphology, is referred to the genus Anachis, and Costoanachis nigricans (Sowerby, 1844), based on anatomy and shell morphology, is transferred to Parvanachis. The resulting seven species of Parvanachis constitute two groups; one (including the type species) with smaller shells and a simple penis morphology, and a group of four larger species with more complex penis morphology.

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PubMed Central

Alvarado-Sizzo, Hernán; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC. PMID:29342184

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

PubMed

Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Seahorses of the Hippocampus coronatus complex: taxonomic revision, and description of Hippocampus haema, a new species from Korea and Japan (Teleostei, Syngnathidae).

PubMed

Han, Sang-Yun; Kim, Jin-Koo; Kai, Yoshiaki; Senou, Hiroshi

2017-01-01

Morphological and molecular analyses were conducted on 182 specimens belonging to the Hippocampus coronatus complex ( H. coronatus sensu lato), collected in Korea and Japan 1933-2015, in order to clarify the taxonomic status of the species within this complex. Three species are recognized based on the shape of the coronet, the number of trunk rings (TrR) and tail rings (TaR), and presence or absence of a wing-tip spine (WS) at the dorsal fin base. Hippocampus coronatus Temminck & Schlegel, 1850 ( H. coronatus sensu stricto), is diagnosed by 10 TrR, 37-40 TaR, an extremely high coronet (55.7-79.0 % head length) with four tips on the corona flat (CoT), and one WS. Hippocampus sindonis Jordan & Snyder, 1901 is diagnosed by 10 TrR, 35-38 TaR, a moderately high coronet (36.3-55.4 % HL) with five CoT, and no WS. A new species, H. haema is described on the basis of 140 specimens, characterized by 10 TrR, 35-38 TaR, a moderately high coronet (34.1-54.9 % head length) with four CoT, and two WS. Hippocampus haema is only known from the Korea Strait, western Kyushu, and East/Japan Sea. Recognition of the three species is supported by differences in mitochondrial DNA fragments (cytochrome b , 16S rRNA, and 12S rRNA).

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Treesearch

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the

An intercomparison of the taxonomic and size composition of tropical macrozooplankton and micronekton collected using three sampling gears

NASA Astrophysics Data System (ADS)

Kwong, Lian E.; Pakhomov, Evgeny A.; Suntsov, Andrey V.; Seki, Michael P.; Brodeur, Richard D.; Pakhomova, Larisa G.; Domokos, Réka

2018-05-01

A micronekton intercalibration experiment was conducted off the southwest coast of Oahu Island, Hawaii in October 2004. Day and night samples were collected in the epipelagic and mesopelagic zones using three micronekton sampling gears: the Cobb Trawl, the Isaacs-Kidd Midwater Trawl (IKMT), and the Hokkaido University Frame Trawl (HUFT). Taxonomic composition and contribution by main size groups to total catch varied among gear types. However, the three gears exhibited similar taxonomic composition for macrozooplankton and micronekton ranging from 20 to 100 mm length (MM20-100). The HUFT and IKMT captured more mesozooplankton and small MM20-100, while the Cobb trawl selected towards larger MM20-100 and nekton. Taxonomic composition was described and inter-compared among gears. The relative efficacy of the three gears was assessed, and size dependent intercalibration coefficients were developed for MM20-100.

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

PubMed Central

Gehring, Philip-Sebastian; Tolley, Krystal A; Eckhardt, Falk Sebastian; Townsend, Ted M; Ziegler, Thomas; Ratsoavina, Fanomezana; Glaw, Frank; Vences, Miguel

2012-01-01

We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision. PMID:22957155

Taxonomic status and paleoecology of Rusingoryx atopocranion (Mammalia, Artiodactyla), an extinct Pleistocene bovid from Rusinga Island, Kenya

NASA Astrophysics Data System (ADS)

Faith, J. Tyler; Choiniere, Jonah N.; Tryon, Christian A.; Peppe, Daniel J.; Fox, David L.

2011-05-01

Rusingoryx atopocranion is a poorly known extinct alcelaphine bovid, documented in Pleistocene deposits associated with Middle Stone Age artifacts on Rusinga Island, Kenya. Following its initial description, Rusingoryx was subsumed into Megalotragus, which includes the extinct giant wildebeests, on the basis of its cranial architecture. Renewed investigations of the Pleistocene deposits on Rusinga Island recovered a large sample of Rusingoryx specimens that provide new taxonomic and paleoecological insight. This study (1) reviews the morphological and phylogenetic evidence concerning the taxonomic status of Rusingoryx and (2) evaluates its paleoecology and dietary habits . The morphology and phylogenetic data indicate that Rusingoryx is distinct from Megalotragus; they likely shared a common ancestor in the late Pliocene. Ecomorphology and mesowear analysis point to a specialized grazing adaptation, and its association with arid-adapted ungulates suggests a preference for arid grasslands. The confirmation of Rusingoryx as a valid taxonomic entity, together with the presence of other extinct taxa (including Megalotragus) on Rusinga Island, suggests an increasingly complex pattern of ungulate biogeography and extinctions in the late Quaternary of East Africa. Rusingoryx appears to have been part of an arid-adapted faunal community that potentially persisted in East Africa until the onset of the Holocene.

Minimal Similarity between Biogeographic Patterns of Morphological Disparity and Taxonomic Richness in Extant Coccolithophores

NASA Astrophysics Data System (ADS)

Villarosa Garcia, M.

2016-02-01

Morphologic disparity, carries both an ecological and evolutionary signal and, where practical, might bridge ecological processes observed in modern seas with macroevolutionary processes observed in the fossil record, complementing taxonomic diversity studies. I compare the biogeography of morphologic disparity and taxonomic richness in extant coccolithophores to understand the role of environmental conditions in their spatial partitioning. I analyze 112 traits in 125 species and measure geographic extent as the occupation of pelagic biogeographic provinces (sensu Spalding et al. 2012). In the modern ocean, coccolithophorid species richness increases towards the equator, peaking in the subtropics, and certain biomes harbor more species. In contrast, their morphologic disparity does not vary across latitudes and biomes, yielding similar values of variance and mean pair-wise distances. Disparity is weakly correlated to richness across clades and biomes (no clear latitudinal pattern). I also study the morphological breadth of clades in a multivariate morphospace plotted as principal coordinate axes (PCO). Clades have distinct centroids but show some overlap in volume. However, they are completely separate when using canonical variates analysis (CVA) on these PCO axes. The centroids of latitudinal groups are closely spaced, and overlap in morphospace, but again separate with CVA. However biome groups can't be distinguished using PCO or CVA. Although clades with the most species tend to have high disparity, most clades are found in every region yielding similar group disparities. Despite the fact that taxonomic diversity is spatially partitioned on the globe, morphologic disparity has no such organization. Past studies using marine gastropods (Roy et al. 2001; McClain 2005), cuttlefish (Neige 2003), and birds (Jønsson et al. 2015) also find minimal support for a biogeographic structure of disparity, highlighting the profound nature of this differential response.

Political complexity predicts the spread of ethnolinguistic groups

PubMed Central

Currie, Thomas E.; Mace, Ruth

2009-01-01

Human languages show a remarkable degree of variation in the area they cover. However, the factors governing the distribution of human cultural groups such as languages are not well understood. While previous studies have examined the role of a number of environmental variables the importance of cultural factors has not been systematically addressed. Here we use a geographical information system (GIS) to integrate information about languages with environmental, ecological, and ethnographic data to test a number of hypotheses that have been proposed to explain the global distribution of languages. We show that the degree of political complexity and type of subsistence strategy exhibited by societies are important predictors of the area covered by a language. Political complexity is also strongly associated with the latitudinal gradient in language area, whereas subsistence strategy is not. We argue that a process of cultural group selection favoring more complex societies may have been important in shaping the present-day global distribution of language diversity. PMID:19380740

Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae)

PubMed Central

Borkenhagen, Kai; Krupp, Friedhelm

2013-01-01

Abstract Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

PubMed

Goldstein, Paul Z; DeSalle, Rob

2011-02-01

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

Predicted taxonomic patterns in pheromone production by longhorned beetles

NASA Astrophysics Data System (ADS)

Ray, Ann M.; Lacey, Emerson S.; Hanks, Lawrence M.

2006-11-01

Males of five species of three tribes in the longhorned beetle subfamily Cerambycinae produce volatile pheromones that share a structural motif (hydroxyl or carbonyl groups at carbons two and three in straight-chains of six, eight, or ten carbons). Pheromone gland pores are present on the prothoraces of males, but are absent in females, suggesting that male-specific gland pores could provide a convenient morphological indication that a species uses volatile pheromones. In this article, we assess the taxonomic distribution of gland pores within the Cerambycinae by examining males and females of 65 species in 24 tribes using scanning electron microscopy. Gland pores were present in males and absent in females of 49 species, but absent in both sexes of the remaining 16 species. Pores were confined to indentations in the cuticle. Among the species that had male-specific gland pores were four species already known to produce volatile compounds consistent with the structural motif. These findings support the initial assumption that gland pores are associated with the production of pheromones by males. There were apparently no taxonomic patterns in the presence of gland pores. These findings suggest that volatile pheromones play an important role in reproduction for many species of the Cerambycinae, and that the trait is evolutionarily labile.

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.

PubMed

Gao, Xiang; Lin, Huaiying; Revanna, Kashi; Dong, Qunfeng

2017-05-10

Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement. We have developed a method that shows significantly improved species-level classification results over existing methods. Our method calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. Taxonomic classifications are assigned from the species to the phylum levels based on the lowest common ancestors of multiple database hits for each query sequence, and further classification reliabilities are evaluated by bootstrap confidence scores. The novelty of our method is that the contribution of each database hit to the taxonomic assignment of the query sequence is weighted by a Bayesian posterior probability based upon the degree of sequence similarity of the database hit to the query sequence. Our method does not need any training datasets specific for different taxonomic groups. Instead only a reference database is required for aligning to the query sequences, making our method easily applicable for different regions of the 16S rRNA gene or other phylogenetic marker genes. Reliable species-level classification for 16S rRNA or other phylogenetic marker genes is critical for microbiome research. Our software shows significantly higher classification accuracy than the existing tools and we provide probabilistic-based confidence scores to evaluate the reliability of our taxonomic classification assignments based on multiple database matches to query sequences. Despite

Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

PubMed

Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

2004-06-01

A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific

PubMed Central

Larkin, Alyse A; Blinebry, Sara K; Howes, Caroline; Lin, Yajuan; Loftus, Sarah E; Schmaus, Carrie A; Zinser, Erik R; Johnson, Zackary I

2016-01-01

The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function. PMID:26800235

Taxa: An R package implementing data standards and methods for taxonomic data

PubMed Central

Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

2018-01-01

The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

Symmetrical group theory for mathematical complexity reduction of digital holograms

NASA Astrophysics Data System (ADS)

Perez-Ramirez, A.; Guerrero-Juk, J.; Sanchez-Lara, R.; Perez-Ramirez, M.; Rodriguez-Blanco, M. A.; May-Alarcon, M.

2017-10-01

This work presents the use of mathematical group theory through an algorithm to reduce the multiplicative computational complexity in the process of creating digital holograms. An object is considered as a set of point sources using mathematical symmetry properties of both the core in the Fresnel integral and the image, where the image is modeled using group theory. This algorithm has multiplicative complexity equal to zero and an additive complexity ( k - 1) × N for the case of sparse matrices and binary images, where k is the number of pixels other than zero and N is the total points in the image.

Digitising legacy zoological taxonomic literature: Processes, products and using the output

PubMed Central

Lyal, Christopher H. C.

2016-01-01

Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

USGS Publications Warehouse

Yasuhara, Moriaki; Stepanova, Anna; Okahashi, Hisayo; Cronin, Thomas M.; Brouwers, Elisabeth M.

2015-01-01

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales.

PubMed

Ceccarelli, Daniela M; Emslie, Michael J; Richards, Zoe T

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales

PubMed Central

Ceccarelli, Daniela M.

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events. PMID:27285160

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

PubMed

Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).

Memory systems, processes, and tasks: taxonomic clarification via factor analysis.

PubMed

Bruss, Peter J; Mitchell, David B

2009-01-01

The nature of various memory systems was examined using factor analysis. We reanalyzed data from 11 memory tasks previously reported in Mitchell and Bruss (2003). Four well-defined factors emerged, closely resembling episodic and semantic memory and conceptual and perceptual implicit memory, in line with both memory systems and transfer-appropriate processing accounts. To explore taxonomic issues, we ran separate analyses on the implicit tasks. Using a cross-format manipulation (pictures vs. words), we identified 3 prototypical tasks. Word fragment completion and picture fragment identification tasks were "factor pure," tapping perceptual processes uniquely. Category exemplar generation revealed its conceptual nature, yielding both cross-format priming and a picture superiority effect. In contrast, word stem completion and picture naming were more complex, revealing attributes of both processes.

Group size and social conflict in complex societies.

PubMed

Shen, Sheng-Feng; Akçay, Erol; Rubenstein, Dustin R

2014-02-01

Conflicts of interest over resources or reproduction among individuals in a social group have long been considered to result in automatic and universal costs to group living. However, exploring how social conflict varies with group size has produced mixed empirical results. Here we develop a model that generates alternative predictions for how social conflict should vary with group size depending on the type of benefits gained from being in a social group. We show that a positive relationship between social conflict and group size is favored when groups form primarily for the benefits of sociality but not when groups form mainly for accessing group-defended resources. Thus, increased social conflict in animal societies should not be viewed as an automatic cost of larger social groups. Instead, studying the relationship between social conflict and the types of grouping benefits will be crucial for understanding the evolution of complex societies.

Bacterial complexes of a high moor related to different elements of microrelief

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Golovchenko, A. V.; Yakushev, A. V.; Yurchenko, E. N.; Manucharov, N. A.; Chernov, I. Yu.

2017-04-01

The analysis of bacterial complexes, including the number, taxonomic composition, physiological state, and proportion of ecological trophic groups was performed in a high moorland related to different elements of the microrelief. The abundance of bacteria, their ability for hydrolysis of polymers and the share of r-strategists were found to be higher in the sphagnum hillocks than on the flat surfaces. The total prokaryote biomass was 4 times greater in the sphagnum samples from microhighs (hillocks). On these elements of the microrelief, the density of actinomycetal mycelium was higher. Bacteria of the hydrolytic complex ( Cytophaga and Chitinophaga genera) were found only in microhigh samples.

A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

PubMed

Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

2016-10-01

Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. Copyright © 2016 Elsevier Inc. All rights reserved.

Taxonomic changes in Solanum section Petota

USDA-ARS?s Scientific Manuscript database

In 1990, the latest comprehensive taxonomic monograph of Solanum section Petota Dumort. recognized 236 species partitioned into 21 series. Of these, 227 were tuber-bearing and nine non-tuber-bearing. NSF-sponsored research has drastically altered knowledge of their species boundaries and interrelati...

Research Review: Evaluating and reformulating the developmental taxonomic theory of antisocial behaviour

PubMed Central

Fairchild, Graeme; Goozen, Stephanie HM; Calder, Andrew J; Goodyer, Ian M

2013-01-01

BackgroundThe developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. MethodsWe conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. ResultsEmpirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). ConclusionsWe conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be

Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

PubMed

Bae, Juhee; Watson, Benjamin

2014-12-01

In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups.

PubMed

Jeuck, Alexandra; Nitsche, Frank; Wylezich, Claudia; Wirth, Olaf; Bergfeld, Tanja; Brutscher, Fabienne; Hennemann, Melanie; Monir, Shahla; Scherwaß, Anja; Troll, Nicole; Arndt, Hartmut

2017-08-01

Heterotrophic flagellates contribute significantly to the matter flux in aquatic and terrestrial ecosystems. Still today their quantification and taxonomic classification bear several problems in field studies, though these methodological problems seem to be increasingly ignored in current ecological studies. Here we describe and test different methods, the live-counting technique, different fixation techniques, cultivation methods like the liquid aliquot method (LAM), and a molecular single cell survey called aliquot PCR (aPCR). All these methods have been tested either using aquatic field samples or cultures of freshwater and marine taxa. Each of the described methods has its advantages and disadvantages, which have to be considered in every single case. With the live-counting technique a detection of living cells up to morphospecies level is possible. Fixation of cells and staining methods are advantageous due to the possible long-term storage and observation of samples. Cultivation methods (LAM) offer the possibility of subsequent molecular analyses, and aPCR tools might complete the deficiency of LAM in terms of the missing detection of non-cultivable flagellates. In summary, we propose a combination of several investigation techniques reducing the gap between the different methodological problems. Copyright © 2017 Elsevier GmbH. All rights reserved.

A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece.

PubMed

Bravakos, Panos; Kotoulas, Georgios; Skaraki, Katerina; Pantazidou, Adriani; Economou-Amilli, Athena

2016-05-01

Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. Copyright © 2016 Elsevier Inc. All rights reserved.

Marine benthic ecological functioning over decreasing taxonomic richness

NASA Astrophysics Data System (ADS)

Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

2015-04-01

Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about

Quantification of complex modular architecture in plants.

PubMed

Reeb, Catherine; Kaandorp, Jaap; Jansson, Fredrik; Puillandre, Nicolas; Dubuisson, Jean-Yves; Cornette, Raphaël; Jabbour, Florian; Coudert, Yoan; Patiño, Jairo; Flot, Jean-François; Vanderpoorten, Alain

2018-04-01

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

PubMed Central

TANIZAWA, Yasuhiro; KOBAYASHI, Hisami; KAMINUMA, Eli; SAKAMOTO, Mitsuo; OHKUMA, Moriya; NAKAMURA, Yasukazu; ARITA, Masanori; TOHNO, Masanori

2017-01-01

Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains. PMID:28748134

Polyphyly of the traditional family Flabellinidae affects a major group of Nudibranchia: aeolidacean taxonomic reassessment with descriptions of several new families, genera, and species (Mollusca, Gastropoda)

PubMed Central

Korshunova, Tatiana; Martynov, Alexander; Bakken, Torkild; Evertsen, Jussi; Fletcher, Karin; Mudianta, I Wayan; Saito, Hiroshi; Lundin, Kennet; Michael Schrödl; Picton, Bernard

2017-01-01

Abstract The Flabellinidae, a heterogeneous assembly of supposedly plesiomorphic to very derived sea slug groups, have not yet been addressed by integrative studies. Here novel material of rarely seen Arctic taxa as well as North Atlantic, North and South Pacific, and tropical Indo-West Pacific flabellinid species is investigated morpho-anatomically and with multi-locus markers (partial COI, 16S rDNA, 28S rDNA and H3) which were generated and analysed in a comprehensive aeolid taxon sampling. It was found that the current family Flabellinidae is polyphyletic and its phylogeny and taxonomic patterns cannot be understood without considering members from all the Aeolidacean families and, based on a robust phylogenetic hypothesis, morpho-anatomical evolution of aeolids is more complex than suspected in earlier works and requires reclassification of the taxon. Morphological diversity of Flabellinidae is corroborated by molecular divergence rates and supports establishing three new families (Apataidae fam. n., Flabellinopsidae fam. n., Samlidae fam. n.), 16 new genera, 13 new species, and two new subspecies among the former Flabellinidae. Two families, namely Coryphellidae and Paracoryphellidae, are restored and traditional Flabellinidae is considerably restricted. The distinctness of the recently described family Unidentiidae is confirmed by both morphological and molecular data. Several species complexes among all ex-“Flabellinidae” lineages are recognised using both morphological and molecular data. The present study shows that Facelinidae and Aeolidiidae, together with traditional “Tergipedidae”, deeply divide traditional “Flabellinidae.” Diagnoses for all aeolidacean families are therefore provided and additionally two new non-flabellinid families (Abronicidae fam. n. and Murmaniidae fam. n.) within traditional tergipedids are established to accommodate molecular and morphological disparity. To address relationships and disparity, we propose a new family

Features of proteolytic properties of tetraphenylporphyrin complex with lanthanide group metals

NASA Astrophysics Data System (ADS)

Tobolkina, Elena A.; Skripnikova, Tatiana A.; Starikova, Anna A.; Shumilova, Galina I.; Pendin, Andrey A.

2018-01-01

Demetallation of metalloporphyrin molecules is one of the essential degradation reactions in photosynthesis. The effect of metalloporphyrin nature on removal of central metals from tetraphenylporphyrin complexes based on lanthanide group metals (Dy, Er, Lu, Ho) has been studied. pH values, at which the metal ions leave the metalloporphyrin complex were established using two-phase spectrophotometric titration with potentiometric pH-control. The pH values decrease with the increase of atomic numbers of lanthanide groups, as well as with increase of 4f-electrons. The reaction of an extra ligand exchange for the hydroxide ion was studied. For Dy-, Er- and Ho-tetraphenylporphyrin complexes one particle of extra ligand coordinates with one porphyrin complex. A complex with dimeric particles can be formed for the system of Lu-tetraphenylporphyrin. Constants of the ion exchange reactions were calculated.

Australian diagnosis related groups: Drivers of complexity adjustment.

PubMed

Jackson, Terri; Dimitropoulos, Vera; Madden, Richard; Gillett, Steve

2015-11-01

In undertaking a major revision to the Australian Refined Diagnosis Related Group (ARDRG) classification, we set out to contrast Australia's approach to using data on additional (not principal) diagnoses with major international approaches in splitting base or Adjacent Diagnosis Related Groups (ADRGs). Comparative policy analysis/narrative review of peer-reviewed and grey literature on international approaches to use of additional (secondary) diagnoses in the development of Australian and international DRG systems. European and US approaches to characterise complexity of inpatient care are well-documented, providing useful points of comparison with Australia's. Australia, with good data sources, has continued to refine its national DRG classification using increasingly sophisticated approaches. Hospital funders in Australia and in other systems are often under pressure from provider groups to expand classifications to reflect clinical complexity. DRG development in most healthcare systems reviewed here reflects four critical factors: these socio-political factors, the quality and depth of the coded data available to characterise the mix of cases in a healthcare system, the size of the underlying population, and the intended scope and use of the classification. Australia's relatively small national population has constrained the size of its DRG classifications, and development has been concentrated on inpatient care in public hospitals. Development of casemix classifications in health care is driven by both technical and socio-political factors. Use of additional diagnoses to adjust for patient complexity and cost needs to respond to these in each casemix application. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

PubMed

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates

Investigating the adiabatic beam grouping at the NICA accelerator complex

NASA Astrophysics Data System (ADS)

Brovko, O. I.; Butenko, A. V.; Grebentsov, A. Yu.; Eliseev, A. V.; Meshkov, I. N.; Svetov, A. L.; Sidorin, A. O.; Slepnev, V. M.

2016-12-01

The NICA complex comprises the Booster and Nuclotron synchrotrons for accelerating particle beams to the required energy and the Collider machine, in which particle collisions are investigated. The experimental heavy-ion program deals with ions up to Au+79. The light-ion program deals with polarized deuterons and protons. Grouping of a beam coasting in an ion chamber is required in many parts of the complex. Beam grouping may effectively increase the longitudinal emittance and particle losses. To avoid these negative effects, various regimes of adiabatic grouping have been simulated and dedicated experiments with a deuteron beam have been conducted at the Nuclotron machine. As a result, we are able to construct and optimize the beam-grouping equipment, which provides a capture efficiency near 100% either retaining or varying the harmonic multiplicity of the HF system.

Connecting the Dots: Social Network Structure, Conflict, and Group Cognitive Complexity

ERIC Educational Resources Information Center

Curseu, Petru L.; Janssen, Steffie E. A.; Raab, Jorg

2012-01-01

The current paper combines arguments from the social capital and group cognition literature to explain two different processes through which communication network structures and intra group conflict influence groups' cognitive complexity (GCC). We test in a sample of 44 groups the mediating role of intra group conflict in the relationship between…

Ylide Ligands as Building Blocks for Bioactive Group 11 Metal Complexes.

PubMed

Gimeno, M Concepción; Johnson, Alice; Marzo, Isabel

2018-05-22

The reactivity of the phosphonium salt, (cyanomethyl)triphenylphosphonium chloride, and the ylide, triphenylphosphoniumcyanomethylide, towards group eleven metal complexes is described. Mononuclear neutral gold(I) and gold(III) complexes of the type [AuX{CH(CN)PPh3}] or [AuX3{CH(CN)PPh3}], and cationic derivatives such as [AuL{CH(CN)PPh3}]X have been prepared. Surprisingly the cationic gold species could only be prepared with ligands with a large steric hindrance such as bulky NHCs or the JohnPhos phosphine, in contrast with silver and copper derivatives which have dimeric structures with coordination to the cyano group of the ylide. Bis(ylide)metal complexes have been synthesised in which a different structure is observed for gold compared to copper and silver. While gold shows mononuclear species, the silver complex presents a bidimensional polymeric structure as a result of further coordination of the silver centre to the nitrogen of the cyano group. These complexes possess two chiral centres and the gold compound is obtained as a mixture of diastereoisomers, whereas the copper and silver derivatives afford only one diastereroisomer. These compounds were screened for the in vitro cytotoxic activity against the human lung carcinoma cell line (A549). The IC50 values reveal an excellent cytotoxic activity for these metal complexes compared with cisplatin. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

PubMed

Kim, S W; Ban, S H; Chung, H J; Choi, D W; Choi, P S; Yoo, O J; Liu, J R

2004-02-01

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

Variance Component Selection With Applications to Microbiome Taxonomic Data.

PubMed

Zhai, Jing; Kim, Juhyun; Knox, Kenneth S; Twigg, Homer L; Zhou, Hua; Zhou, Jin J

2018-01-01

High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator) penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV) infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

PubMed Central

Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

Diversity of Phylogenetic Information According to the Locus and the Taxonomic Level: An Example from a Parasitic Mesostigmatid Mite Genus

PubMed Central

Roy, Lise; Dowling, Ashley P.G.; Chauve, Claude Marie; Buronfosse, Thierry

2010-01-01

Molecular markers for cladistic analyses may perform differently according to the taxonomic group considered and the historical level under investigation. Here we evaluate the phylogenetic potential of five different markers for resolving evolutionary relationships within the ectoparasitic genus Dermanyssus at the species level, and their ability to address questions about the evolution of specialization. COI provided 9–18% divergence between species (up to 9% within species), 16S rRNA 10–16% (up to 4% within species), ITS1 and 2 2–9% (up to 1% within species) and Tropomyosin intron n 8–20% (up to 6% within species). EF-1α revealed different non-orthologous copies within individuals of Dermanyssus and Ornithonyssus. Tropomyosin intron n was shown containing consistent phylogenetic signal at the specific level within Dermanyssus and represents a promising marker for future prospects in phylogenetics of Acari. Phylogenetic analyses revealed that the generalist condition is apomorphic and D. gallinae might represent a complex of hybridized lineages. The split into hirsutus-group and gallinae-group in Dermanyssus does not seem to be appropriate based upon these results and D. longipes appears to be composed of two different entities. PMID:20480038

Infrared Multiple-Photon Dissociation spectroscopy of group II metal complexes with salicylate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan P. Dain; Gary Gresham; Gary S. Groenewold

2011-07-01

Ion-trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations were used to characterize singly-charged, 1:1 complexes of Ca2+, Sr2+ and Ba2+ with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO2 and (b) formation of [MOH]+ where M=Ca2+, Sr2+ or Ba2+. DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cationmore » is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 – 1650 cm-1, and the best correlation between theoretical and experimental spectra for the structure that features coordination of the metal ion by phenoxide and the carbonyl group of the carboxylic acid group, consistent with calculated energies for the respective species.« less

The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

PubMed Central

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

PubMed

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

Group 4 Metalloporphyrin diolato Complexes and Catalytic Application of Metalloporphyrins and Related Transition Metal Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Guodong

In this work, the first examples of group 4 metalloporphyrin 1,2-diolato complexes were synthesized through a number of strategies. In general, treatment of imido metalloporphyrin complexes, (TTP)M=NR, (M = Ti, Zr, Hf), with vicinal diols led to the formation of a series of diolato complexes. Alternatively, the chelating pinacolate complexes could be prepared by metathesis of (TTP)MCl 2 (M = Ti, Hf) with disodium pinacolate. These complexes were found to undergo C-C cleavage reactions to produce organic carbonyl compounds. For titanium porphyrins, treatment of a titanium(II) alkyne adduct, (TTP)Ti(η 2-PhC≡CPh), with aromatic aldehydes or aryl ketones resulted in reductive couplingmore » of the carbonyl groups to produce the corresponding diolato complexes. Aliphatic aldehydes or ketones were not reactive towards (TTP)Ti(η 2-PhC≡CPh). However, these carbonyl compounds could be incorporated into a diolato complex on reaction with a reactive precursor, (TTP)Ti[O(Ph) 2C(Ph) 2O] to provide unsymmetrical diolato complexes via cross coupling reactions. In addition, an enediolato complex (TTP)Ti(OCPhCPhO) was obtained from the reaction of (TTP)Ti(η 2-PhC≡CPh) with benzoin. Titanium porphyrin diolato complexes were found to be intermediates in the (TTP)Ti=O-catalyzed cleavage reactions of vicinal diols, in which atmospheric oxygen was the oxidant. Furthermore, (TTP)Ti=O was capable of catalyzing the oxidation of benzyl alcohol and α-hydroxy ketones to benzaldehyde and α-diketones, respectively. Other high valent metalloporphyrin complexes also can catalyze the oxidative diol cleavage and the benzyl alcohol oxidation reactions with dioxygen. A comparison of Ti(IV) and Sn(IV) porphyrin chemistry was undertaken. While chelated diolato complexes were invariably obtained for titanium porphyrins on treatment with 1,2-diols, the reaction of vicinal diols with tin porphyrins gave a number of products, including mono-, bis-alkoxo, and chelating diolato complexes

Modeling complex tone perception: grouping harmonics with combination-sensitive neurons.

PubMed

Medvedev, Andrei V; Chiao, Faye; Kanwal, Jagmeet S

2002-06-01

Perception of complex communication sounds is a major function of the auditory system. To create a coherent precept of these sounds the auditory system may instantaneously group or bind multiple harmonics within complex sounds. This perception strategy simplifies further processing of complex sounds and facilitates their meaningful integration with other sensory inputs. Based on experimental data and a realistic model, we propose that associative learning of combinations of harmonic frequencies and nonlinear facilitation of responses to those combinations, also referred to as "combination-sensitivity," are important for spectral grouping. For our model, we simulated combination sensitivity using Hebbian and associative types of synaptic plasticity in auditory neurons. We also provided a parallel tonotopic input that converges and diverges within the network. Neurons in higher-order layers of the network exhibited an emergent property of multifrequency tuning that is consistent with experimental findings. Furthermore, this network had the capacity to "recognize" the pitch or fundamental frequency of a harmonic tone complex even when the fundamental frequency itself was missing.

Research review: evaluating and reformulating the developmental taxonomic theory of antisocial behaviour.

PubMed

Fairchild, Graeme; van Goozen, Stephanie H M; Calder, Andrew J; Goodyer, Ian M

2013-09-01

The developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. We conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. Empirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). We conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be quantitative, rather than qualitative, in

Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae).

PubMed

Bourguignon, Thomas; Šobotník, Jan; Hanus, Robert; Krasulová, Jana; Vrkoslav, Vladimír; Cvačka, Josef; Roisin, Yves

2013-12-01

Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species. Copyright © 2013 Elsevier Inc. All rights reserved.

Ongoing Speciation and Gene Flow between Taxonomically Challenging Trochulus Species Complex (Gastropoda: Hygromiidae).

PubMed

Proćków, Małgorzata; Strzała, Tomasz; Kuźnik-Kowalska, Elżbieta; Proćków, Jarosław; Mackiewicz, Paweł

2017-01-01

Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy. We used an integrated approach based on morphological features, ecological preferences and two molecular markers: mitochondrial COI sequences and microsatellites. Comparison of these results demonstrated: (i) conchological distinction of T. striolatus and T. sericeus; (ii) anatomical, ecological and genetic differentiation of T. graminicola and (iii) concordance between morphological characters and mtDNA markers in T. striolatus. Moreover, our data showed an intricate evolutionary history within the genus Trochulus, which can be best explained by: (i) recent or ongoing gene flow between taxa or (ii) their large ancestral polymorphism. Both of these hypotheses suggest that diversification within this group of snails has occurred relatively recently. The mismatches between species defined on morphology and on molecular genetics indicate the complexity of the processes involved in the diversification of this genus.

Ongoing Speciation and Gene Flow between Taxonomically Challenging Trochulus Species Complex (Gastropoda: Hygromiidae)

PubMed Central

Proćków, Małgorzata; Strzała, Tomasz; Kuźnik-Kowalska, Elżbieta; Proćków, Jarosław; Mackiewicz, Paweł

2017-01-01

Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy. We used an integrated approach based on morphological features, ecological preferences and two molecular markers: mitochondrial COI sequences and microsatellites. Comparison of these results demonstrated: (i) conchological distinction of T. striolatus and T. sericeus; (ii) anatomical, ecological and genetic differentiation of T. graminicola and (iii) concordance between morphological characters and mtDNA markers in T. striolatus. Moreover, our data showed an intricate evolutionary history within the genus Trochulus, which can be best explained by: (i) recent or ongoing gene flow between taxa or (ii) their large ancestral polymorphism. Both of these hypotheses suggest that diversification within this group of snails has occurred relatively recently. The mismatches between species defined on morphology and on molecular genetics indicate the complexity of the processes involved in the diversification of this genus. PMID:28107432

The Effects of Gender Variety and Power Disparity on Group Cognitive Complexity in Collaborative Learning Groups

ERIC Educational Resources Information Center

Curseu, Petru Lucian; Sari, Kimzana

2015-01-01

This study sets up to test the extent to which gender variety moderates the impact of power disparity on group cognitive complexity (GCC) and satisfaction with the group in a collaborative learning setting. Using insights from gender differences in perceptions, orientations and conflict handling behavior in negotiation, as well as gender…

Taxonomic triage and the poverty of phylogeny.

PubMed Central

Wheeler, Quentin D

2004-01-01

Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

PubMed

Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

2017-01-31

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)

PubMed Central

Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

2015-01-01

The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units. PMID:26029257

Application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment.

PubMed

Xu, Henglong; Jiang, Yong; Al-Rasheid, Khaled A S; Al-Farraj, Saleh A; Song, Weibo

2011-08-01

Ciliated protozoa play important roles in aquatic ecosystems especially regarding their functions in micro-food web and have many advantages in environmental assessment compared with most other eukaryotic organisms. The aims of this study were focused on analyzing the application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment. The spatial taxonomic patterns and diversity measures in response to physical-chemical variables were studied based on data from samples collected during 1-year cycle in the semi-enclosed Jiaozhou Bay, northern China. The spatial patterns of ciliate communities were significantly correlated with the changes of environmental status. The taxonomic distinctness (Δ*) and the average taxonomic distinctness (Δ+) were significantly negatively correlated with the changes of nutrients (e.g., nitrate nitrogen and soluble active phosphate; P<0.05). Pairwise indices of Δ+ and the variation in taxonomic distinctness (Λ+) showed a decreasing trend of departure from the expected taxonomic breadth in response to the eutrophication stress and anthropogenic impact. The taxonomic relatedness (especially the pairwise Δ+ and Λ+) indices of ciliate communities are robust as an indicator with scientifically operational value in marine environmental assessment.

Functional group diversity is key to Southern Ocean benthic carbon pathways

PubMed Central

Sands, Chester J.

2017-01-01

High latitude benthos are globally important in terms of accumulation and storage of ocean carbon, and the feedback this is likely to have on regional warming. Understanding this ecosystem service is important but difficult because of complex taxonomic diversity, history and geography of benthic biomass. Using South Georgia as a model location (where the history and geography of benthic biology is relatively well studied) we investigated whether the composition of functional groups were critical to benthic accumulation, immobilization and burial pathway to sequestration–and also aid their study through simplification of identification. We reclassified [1], [2]) morphotype and carbon mass data to 13 functional groups, for each sample of 32 sites around the South Georgia continental shelf. We investigated the influence on carbon accumulation, immobilization and sequestration estimate by multiple factors including the compositions of functional groups. Functional groups showed high diversity within and between sites, and within and between habitat types. Carbon storage was not linked to a functional group in particular but accumulation and immobilization increased with the number of functional groups present and the presence of hard substrata. Functional groups were also important to carbon burial rate, which increased with the presence of mixed (hard and soft substrata). Functional groups showed high surrogacy for taxonomic composition and were useful for examining contrasting habitat categorization. Functional groups not only aid marine carbon storage investigation by reducing time and the need for team size and speciality, but also important to benthic carbon pathways per se. There is a distinct geography to seabed carbon storage; seabed boulder-fields are hotspots of carbon accumulation and immobilization, whilst the interface between such boulder-fields and sediments are key places for burial and sequestration. PMID:28654664

Complex Cooperative Strategies in Group-Territorial African Lions

NASA Astrophysics Data System (ADS)

Heinsohn, Robert; Packer, Craig

1995-09-01

Female lions (Panthera leo) showed persistent individual differences in the extent to which they participated in group-territorial conflict. When intergroup encounters were simulated by playback of aggressive vocalizations, some individuals consistently led the approach to the recorded intruder, whereas others lagged behind and avoided the risks of fighting. The lead females recognized that certain companions were laggards but failed to punish them, which suggests that cooperation is not maintained by reciprocity. Modification of the "odds" in these encounters revealed that some females joined the group response when they were most needed, whereas other lagged even farther behind. The complexity of these responses emphasizes the great diversity of individual behavior in this species and the inadequacy of current theory to explain cooperation in large groups.

Complex contexts and relationships affect clinical decisions in group therapy.

PubMed

Tasca, Giorgio A; Mcquaid, Nancy; Balfour, Louise

2016-09-01

Clinical errors tend to be underreported even though examining them can provide important training and professional development opportunities. The group therapy context may be prone to clinician errors because of the added complexity within which therapists work and patients receive treatment. We discuss clinical errors that occurred within a group therapy in which a patient for whom group was not appropriate was admitted to the treatment and then was not removed by the clinicians. This was countertherapeutic for both patient and group. Two clinicians were involved: a clinical supervisor who initially assessed and admitted the patient to the group, and a group therapist. To complicate matters, the group therapy occurred within the context of a clinical research trial. The errors, possible solutions, and recommendations are discussed within Reason's Organizational Accident Model (Reason, 2000). In particular, we discuss clinician errors in the context of countertransference and clinician heuristics, group therapy as a local work condition that complicates clinical decision-making, and the impact of the research context as a latent organizational factor. We also present clinical vignettes from the pregroup preparation, group therapy, and supervision. Group therapists are more likely to avoid errors in clinical decisions if they engage in reflective practice about their internal experiences and about the impact of the context in which they work. Therapists must keep in mind the various levels of group functioning, especially related to the group-as-a-whole (i.e., group composition, cohesion, group climate, and safety) when making complex clinical decisions in order to optimize patient outcomes. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Communication Network Integration and Group Uniformity in a Complex Organization.

ERIC Educational Resources Information Center

Danowski, James A.; Farace, Richard V.

This paper contains a discussion of the limitations of research on group processes in complex organizations and the manner in which a procedure for network analysis in on-going systems can reduce problems. The research literature on group uniformity processes and on theoretical models of these processes from an information processing perspective…

Complex network construction based on user group attention sequence

NASA Astrophysics Data System (ADS)

Zhang, Gaowei; Xu, Lingyu; Wang, Lei

2018-04-01

In the traditional complex network construction, it is often to use the similarity between nodes, build the weight of the network, and finally build the network. However, this approach tends to focus only on the coupling between nodes, while ignoring the information transfer between nodes and the transfer of directionality. In the network public opinion space, based on the set of stock series that the network groups pay attention to within a certain period of time, we vectorize the different stocks and build a complex network.

The Role of Social Identity Complexity in Inter-Group Attitudes among Young Adolescents

ERIC Educational Resources Information Center

Knifsend, Casey A.; Juvonen, Jaana

2013-01-01

To supplement research on adolescent social identities, the current study examined how social identity complexity relates to ethnic inter-group attitudes in a young adolescent sample (N = 97; "age range" = 12-14 years). Social identity complexity refers to the perceived overlap of groups with which youth align themselves. Descriptive…

Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

PubMed

Liyanage, K K; Khan, Sehroon; Brooks, Siraprapa; Mortimer, Peter E; Karunarathna, Samantha C; Xu, Jianchu; Hyde, Kevin D

2017-04-01

Powdery mildew is a fungal disease that infects a wide range of plants, including rubber trees, which results in a reduction of latex yields of up to 45%. The causal agent of powdery mildew of rubber was first described as Oidium heveae, but later morpho-molecular research suggested that in the past, O. heveae has been confused with Erysiphe quercicola. However, it is still under debate whether the causal agent should be classified as a species of the genus Erysiphe emend. or Golovinomyces and Podosphaera, respectively. Therefore, the aim of this study was to undertake the morpho-molecular characterization of powdery mildew species associated with rubber trees, thus resolving these taxonomic issues. Morphological observation under light and scanning electron microscopes (SEM) clearly identified two morphotypes of the rubber powdery mildew. With the support of morphological and phylogenetic data, one of the two morphotypes was identified as the asexual morph of E. quercicola, while the second morphotype is still insufficiently known and according to the morphological results obtained we assume that it might belong to the genus Golovinomyces. More collections and additional molecular data are required for final conclusions regarding the exact taxonomic position of the second morphotype of rubber powdery mildew and its relation to the name O. heveae. The haplotype analysis identified eight haplotype groups of E. quercicola indicating the high genetic diversity of the species. Copyright © 2017 Elsevier Ltd. All rights reserved.

DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.

PubMed

Lara, Ariagna; Ponce de León, José Luis; Rodríguez, Rodet; Casane, Didier; Côté, Guillaume; Bernatchez, Louis; García-Machado, Erik

2010-05-01

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention. © 2009 Blackwell Publishing Ltd.

Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).

PubMed

Musher, Lukas J; Cracraft, Joel

2018-01-01

Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized. Copyright © 2017 Elsevier Inc. All rights reserved.

Infrared multiple-photon dissociation spectroscopy of group II metal complexes with salicylate.

PubMed

Dain, Ryan P; Gresham, Gary; Groenewold, Gary S; Steill, Jeffrey D; Oomens, Jos; van Stipdonk, Michael J

2011-07-15

Ion trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations, were used to characterize singly charged, 1:1 complexes of Ca(2+), Sr(2+) and Ba(2+) with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO(2) and (b) formation of [MOH](+) where M = Ca(2+), Sr(2+) or Ba(2+). DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cation is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 and 1650 cm(-1), and the best correlation between theoretical and experimental spectra is found for the structure that features coordination of the metal ion by phenoxide and the carbonyl O of the carboxylic acid group, consistent with the calculated energies for the respective species. Copyright © 2011 John Wiley & Sons, Ltd.

Stratification of co-evolving genomic groups using ranked phylogenetic profiles

PubMed Central

Freilich, Shiri; Goldovsky, Leon; Gottlieb, Assaf; Blanc, Eric; Tsoka, Sophia; Ouzounis, Christos A

2009-01-01

Background Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. Results The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. Conclusion Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples. PMID:19860884

Contrasting Taxonomic and Phylogenetic Diversity Responses to Forest Modifications: Comparisons of Taxa and Successive Plant Life Stages in South African Scarp Forest

PubMed Central

Grass, Ingo; Brandl, Roland; Botzat, Alexandra; Neuschulz, Eike Lena; Farwig, Nina

2015-01-01

The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

PubMed Central

Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P.; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

2016-01-01

The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR. PMID:26915094

Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

ERIC Educational Resources Information Center

Srinivasan, Mahesh; Snedeker, Jesse

2014-01-01

How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

Emergent sensing of complex environments by mobile animal groups.

PubMed

Berdahl, Andrew; Torney, Colin J; Ioannou, Christos C; Faria, Jolyon J; Couzin, Iain D

2013-02-01

The capacity for groups to exhibit collective intelligence is an often-cited advantage of group living. Previous studies have shown that social organisms frequently benefit from pooling imperfect individual estimates. However, in principle, collective intelligence may also emerge from interactions between individuals, rather than from the enhancement of personal estimates. Here, we reveal that this emergent problem solving is the predominant mechanism by which a mobile animal group responds to complex environmental gradients. Robust collective sensing arises at the group level from individuals modulating their speed in response to local, scalar, measurements of light and through social interaction with others. This distributed sensing requires only rudimentary cognition and thus could be widespread across biological taxa, in addition to being appropriate and cost-effective for robotic agents.

Chinese deaf adolescents' free recall of taxonomic, slot-filler, and thematic categories.

PubMed

Li, Degao; Zhang, Jijia

2009-08-01

Four experiments were conducted to show that deaf adolescents tended to process information in different ways from hearing adolescents. Memorizing items sequentially shown on computer screens under the control of their articulators' movements, deaf adolescents tended to treat items that cohered as taxonomic, thematic, or slot-filler categories as isolated pieces of information. Having to perceive information by means of sign language, however, their achievements were not worse than those of hearing adolescents anymore, no matter whether the stimuli were presented as words or pictures. They could not only utilize categories relations to help memorize categories exemplars but were relatively better aware of slot-filler or thematic than taxonomic relations as well, suggesting that they had a relatively delayed development of taxonomic category representations in comparison with hearing adolescents.

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

PubMed Central

Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

2009-01-01

Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference

Solar-phase-angle effects on the taxonomic classification of asteroids

NASA Astrophysics Data System (ADS)

Carvano, J.; Davallos, J.

2014-07-01

Asteroid taxonomy is the effort of grouping asteroids into classes based on similarities of a number of their observational properties. The most used properties include measurements of their spectral reflectance (by means of low-resolution spectra, spectro-photometry, or colors), and geometric albedo. The usefulness of asteroid taxonomic classes derived in this way relies on the assumption that the classes bear some correspondence to the mineralogy of the asteroids, and on the fact that such classification can be made using types of observations that presently are available to a large number of asteroids. Therefore, asteroid taxonomy can be used to infer trends in the distribution of compositions in the main belt and other populations, as an additional parameter in defining asteroid families, and as a selection tool to identify candidates for more detailed observations. However, the fact that the correspondence between taxonomic class and composition is far from perfect is still sometimes overlooked in the literature. Indeed, although a taxonomic classification narrows down the possible mineralogies of a given asteroid, it will seldom point univocally to one particular mineralogy. This happens for a number of reasons, some linked to the intrinsic difficulty involved in the remote characterization of the mineralogy of an asteroid, since it depends on the presence of absorption bands in its reflectance spectrum which may be absent or not completely sampled by the observations used to derive taxonomy. Other problem here is the exposure of the material on the surface of the asteroid to space-weathering effects, such as solar wind implantation and micro-meteorite bombardment, which can change the optical properties of the material. Finally, the overall shape of the reflectance spectrum of an asteroid is also affected by the geometry of the observation, as well as by its shape. In this work, we analyze how the classification of asteroids observed by the Sloan Digital Sky

Genotypic relationships among strains classified under the (Pasteurella) haemolytica-complex as indicated by ribotyping and multilocus enzyme electrophoresis.

PubMed

Angen, O; Caugant, D A; Olsen, J E; Bisgaard, M

1997-10-01

Two-hundred and one strains classified under the (Pasteurella) haemolytica-complex isolated from cattle, sheep, deer, pigs, hares and rabbits were investigated by ribotyping. Fifty-nine of these strains were selected for further studies using multilocus enzyme electrophoresis (MEE). A correlation between the clusters identified by ribotyping and MEE was demonstrated and the results furthermore indicated that a genetic basis exists for most clusters previously outlined by the use of quantitative evaluation of phenotypic data. The taxonomic relevance of ornithine decarboxylase and fermentation of L-arabinose, D-sorbitol and glucosides for taxonomic delineation within the (P.) haemolytica-complex was supported. A taxonomic importance was further indicated for ONPG, ONPX, ONPF, meso-inositol, D-xylose, maltose, dextrine and NPG in relation to some of the taxa. Within the porcine taxon 15, however, differences in ornithine decarboxylase did not correspond to genetic clusters. Six lineages were revealed by MEE. Lineage A contained electrophoretic types (ETs) representing biogroups 1, 3A-3H, 8A and 9, indicating a genetic relationship between these groups--an observation which was supported by ribotyping. Lineage B included biogroup 8D, 3 strains from biogroup 10 and a single strain from biogroup 1 and taxon 18/biovar 1. Lineage C contained strains allocated to biogroup 6 from ruminants and the porcine taxon 15. The similarity between these two groups was accentuated by ribotyping. Lineage D and the single isolate in lineage E contained strains allocated to biogroups 7, 10, 8B and 8C, in addition to single strains from biogroups 6 and 9. The same strains were found in the heterogenous ribotype cluster 17. Lineage F contained strains representing the leprine taxon 20 and the ruminant (P.) granulomatis. Ribotyping indicated that the ruminant biogroup 3J was affiliated with both taxon 20 and (P.) granulomatis.

Phylogenetic disassembly of species boundaries in a widespread group of Australian skinks (Scincidae: Ctenotus).

PubMed

Rabosky, Daniel L; Hutchinson, Mark N; Donnellan, Stephen C; Talaba, Amanda L; Lovette, Irby J

2014-08-01

Scincid lizards in the genus Ctenotus represent one of Australia's most species-rich vertebrate clades, with more than 100 recognized species. Formal diagnoses of many species have relied on qualitative assessments of adult color pattern, but the validity of many such species has not been tested in a phylogenetic framework. We used mitochondrial and nuclear DNA to perform the first phylogenetic analysis of species in the Ctenotus inornatus group, a complex of at least 11 nominal forms that are distributed widely across the Australian continent. Mitochondrial and nuclear gene phylogenies support the presence of multiple species in the group, but these clades largely fail to match species boundaries as currently defined. Multivariate analyses of color pattern indicate that extreme intraspecific morphological variation in this character has created a significant impediment to understanding taxonomic diversity in the group. Our results suggest that nearly all species in the C. inornatus group require substantial taxonomic revision, and several geographically widespread forms ("C. saxatilis" and "C. robustus") appear to be polyphyletic taxa drawn from phenotypically similar but genetically distinct lineages. We describe one new species and provide redescriptions for three additional species. We synonymize names applied to a number of genetically incoherent or otherwise poorly-defined forms. The results of our study highlight an acute need for population genetic studies of species boundaries in Australian skinks, many of which are recognized by morphological traits that vary greatly within and between populations. Copyright © 2014 Elsevier Inc. All rights reserved.

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

PubMed

Clarke, Laurence J; Soubrier, Julien; Weyrich, Laura S; Cooper, Alan

2014-11-01

Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

Lateral gene transfer and the origins of prokaryotic groups.

PubMed

Boucher, Yan; Douady, Christophe J; Papke, R Thane; Walsh, David A; Boudreau, Mary Ellen R; Nesbø, Camilla L; Case, Rebecca J; Doolittle, W Ford

2003-01-01

Lateral gene transfer (LGT) is now known to be a major force in the evolution of prokaryotic genomes. To date, most analyses have focused on either (a) verifying phylogenies of individual genes thought to have been transferred, or (b) estimating the fraction of individual genomes likely to have been introduced by transfer. Neither approach does justice to the ability of LGT to effect massive and complex transformations in basic biology. In some cases, such transformation will be manifested as the patchy distribution of a seemingly fundamental property (such as aerobiosis or nitrogen fixation) among the members of a group classically defined by the sharing of other properties (metabolic, morphological, or molecular, such as small subunit ribosomal RNA sequence). In other cases, the lineage of recipients so transformed may be seen to comprise a new group of high taxonomic rank ("class" or even "phylum"). Here we review evidence for an important role of LGT in the evolution of photosynthesis, aerobic respiration, nitrogen fixation, sulfate reduction, methylotrophy, isoprenoid biosynthesis, quorum sensing, flotation (gas vesicles), thermophily, and halophily. Sometimes transfer of complex gene clusters may have been involved, whereas other times separate exchanges of many genes must be invoked.

Evaluative and Taxonomic Encoding in Children's Memory.

ERIC Educational Resources Information Center

Kail, Robert V., Jr.; Schroll, John T.

Two experiments were conducted to investigate the development of evaluative and taxonomic encoding in children's memory. The task used was a modification of the Wickens short-term memory task in which subjects' recall of words is tested following a distraction task. The first experiment found that 11-year-old children, but not 8-year-old children,…

Rapid evolution in lekking grouse: Implications for taxonomic definitions

USGS Publications Warehouse

Oyler-McCance, Sara J.; St. John, Judy; Quinn, Thomas W.

2010-01-01

Species and subspecies delineations were traditionally defined by morphological and behavioral traits, as well as by plumage characteristics. Molecular genetic data have more recently been used to assess these classifications and, in many cases, to redefine them. The recent practice of utilizing molecular genetic data to examine taxonomic questions has led some to suggest that molecular genetic methods are more appropriate than traditional methods for addressing taxonomic uncertainty and management units. We compared the North American Tetraoninae—which have been defined using plumage, morphology, and behavior—and considered the effects of redefinition using only neutral molecular genetic data (mitochondrial control region and cytochrome oxidase subunit 1). Using the criterion of reciprocal monophyly, we failed to recognize the five species whose mating system is highly polygynous, with males displaying on leks. In lek-breeding species, sexual selection can act to influence morphological and behavioral traits at a rate much faster than can be tracked genetically. Thus, we suggest that at least for lek-breeding species, it is important to recognize the possibility that morphological and behavioral changes may occur at an accelerated rate compared with the processes that led to reciprocal monophyly of putatively neutral genetic markers. Therefore, it is particularly important to consider the possible disconnect between such lines of evidence when making taxonomic revisions and definitions of management units.

taxonomic diversity and pest vulnerability in street tree assemblages

EPA Pesticide Factsheets

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle??s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in ur

Polycomb group protein complexes exchange rapidly in living Drosophila.

PubMed

Ficz, Gabriella; Heintzmann, Rainer; Arndt-Jovin, Donna J

2005-09-01

Fluorescence recovery after photobleaching (FRAP) microscopy was used to determine the kinetic properties of Polycomb group (PcG) proteins in whole living Drosophila organisms (embryos) and tissues (wing imaginal discs and salivary glands). PcG genes are essential genes in higher eukaryotes responsible for the maintenance of the spatially distinct repression of developmentally important regulators such as the homeotic genes. Their absence, as well as overexpression, causes transformations in the axial organization of the body. Although protein complexes have been isolated in vitro, little is known about their stability or exact mechanism of repression in vivo. We determined the translational diffusion constants of PcG proteins, dissociation constants and residence times for complexes in vivo at different developmental stages. In polytene nuclei, the rate constants suggest heterogeneity of the complexes. Computer simulations with new models for spatially distributed protein complexes were performed in systems showing both diffusion and binding equilibria, and the results compared with our experimental data. We were able to determine forward and reverse rate constants for complex formation. Complexes exchanged within a period of 1-10 minutes, more than an order of magnitude faster than the cell cycle time, ruling out models of repression in which access of transcription activators to the chromatin is limited and demonstrating that long-term repression primarily reflects mass-action chemical equilibria.

Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

DTIC Science & Technology

2001-09-30

1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

H 2-saturation of high affinity H 2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

DOE PAGES

Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.; ...

2016-03-10

Soil microbial communities are continuously exposed to H 2 diffusing into the soil from the atmosphere. N 2-fixing nodules represent a peculiar microniche in soil where H 2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H 2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H 2 exposure from the atmosphere and N 2-fixing nodules. Biphasic kinetic parameters governing H 2 oxidation activity in soil changed drastically upon elevated H 2 exposure, corresponding to a slight but significant decay ofmore » high affinity H 2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H 2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H 2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H 2 exposure, suggesting that H 2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H 2-rich environments exert a direct influence on soil H 2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.« less

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

PubMed Central

Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.

2016-01-01

Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities. PMID:26989620

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

PubMed Central

Dröge, J.; Gregor, I.; McHardy, A. C.

2015-01-01

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

Current knowledge of the species complex Anastrepha fraterculus (Diptera, Tephritidae) in Brazil

PubMed Central

Vaníčková, Lucie; Hernández-Ortiz, Vicente; Bravo, Iara Sordi Joachim; Dias, Vanessa; Roriz, Alzira Kelly Passos; Laumann, Raul Alberto; Mendonça, Adriana de Lima; Paranhos, Beatriz Aguiar Jordão; do Nascimento, Ruth Rufino

2015-01-01

Abstract The study of the species complex Anastrepha fraterculus (Af complex) in Brazil is especially important in a taxonomical, evolutionary and pest management context, because there are evidences that some of them may occur in sympatry. In this review, we analyzed the main results supporting evidences that three cryptic species occur in Brazil. The taxonomical and phylogenetic relationships based on eggshell morphology, adult morphometrics, as well as cytotaxonomy and genetic differentiations are discussed. We also review available information on sexual behavior including acoustic communication of males during courtship and sexual incompatibility; and chemical signals involved in the communication between sexes, with a special focus on sex pheromones. We examined the role of long- and short-range pheromones (male-produced volatiles and cuticular hydrocarbons, respectively), their implications in sexual isolation, and their possible use for chemotaxonomic differentiation of the putative species of the Af complex. PMID:26798261

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

PubMed Central

Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

2013-01-01

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

PubMed Central

Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

2012-01-01

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

Chinese deaf and hard of hearing adolescents' awareness of thematic and taxonomic relations among ordinary concepts represented by pictures and written words.

PubMed

Li, Degao; Gao, Kejuan; Zhang, Yue; Wu, Xueyun

2012-01-01

Inspired by a previous study of Korean deaf and hard of hearing adolescents, the researchers conducted a priming task of living-nonliving categorization with a sample of Chinese deaf and hard of hearing adolescents. The sample in this study had significantly lower accuracy levels for the thematically related items than for the taxonomically related items and significantly larger differences in reaction times than a group of hearing adolescents when stimuli were changed from pictures to written words. However, they were not significantly different from the hearing adolescents in their performance with the taxonomically related written words. Furthermore, unlike the hearing adolescents, they did not have significantly different reaction times as the result of changes in positions of stimulus presentations.

Molecular systematics, species delimitation and diversification patterns of the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico.

PubMed

Ramírez-Reyes, Tonatiuh; Piñero, Daniel; Flores-Villela, Oscar; Vázquez-Domínguez, Ella

2017-10-01

The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation of geckos belonging to the genus Phyllodactylus is still controversial, 16 of which are distributed in Mexico and 13 are endemic. Although the large morphological variation shown by the Phyllodactylus species from Mexico has been amply documented, little is known about their genetic diversity and evolutionary relationships, and much less regarding cryptic speciation. Here, we included the most comprehensive sampling of populations and species of the Phyllodactylus lanei complex distributed in Mexico, and applied an analytical approach that included probabilistic phylogenetic analyses, jointly with species delimitation methods and Bayesian putative species validation analysis. Our results suggest the existence of 10 lineages within the complex, supporting the existence of cryptic species, and in great contrast with the current taxonomic proposal that includes only four subspecies. The most recent common ancestor (MRCA) for the P. lanei clade originated on the Early Eocene (∼54Mya), along the southern coasts of Mexico, followed by the highest diversification of the complex MRCA during the Eocene (34-56Mya). Lineages subsequently dispersed and diversified towards the northwest, and the diversification process ended with the most recent lineages inhabiting two islands on the coasts of Nayarit (Miocene; 5.5-23Mya). Our results highlight three vicariant events associated with the evolution of the lineages, two of them intimately related to the formation of the Sierra Madre del Sur and the Transmexican Volcanic Belt mountain ranges, main geographic barriers that isolated and facilitated the divergence and speciation in this group of geckos. Finally, we

Taxonomic review of the Ornithocheirus complex (Pterosauria) from the Cretaceous of England

PubMed Central

Rodrigues, Taissa; Kellner, Alexander Wilhelm Armin

2013-01-01

Abstract Over a decade after the last major review of the Cambridge Greensand pterosaurs, their systematics remains one of the most disputed points in pterosaur taxonomy. Ornithocheiridae is still a wastebasket for fragmentary taxa, and some nomenclatural issues are still a problem. Here, the species from the Cretaceous of England that, at some point, were referred in Ornithocheirus, are reviewed. Investigation of the primary literature confirmed that Criorhynchus should be considered an objective junior synonym of Ornithocheirus. Taxonomic review of more than 30 species known from fragmentary remains showed that 16 of them are undiagnosable (nomina dubia): Palaeornis cliftii, Cimoliornis diomedeus, Pterodactylus compressirostris, Pterodactylus fittoni, Pterodactylus woodwardi, Ornithocheirus brachyrhinus, Ornithocheirus carteri, Ornithocheirus crassidens, Ornithocheirus dentatus, Ornithocheirus enchorhynchus, Ornithocheirus eurygnathus, Ornithocheirus oxyrhinus, Ornithocheirus scaphorhynchus, Ornithocheirus tenuirostris, Ornithocheirus xyphorhynchus, and Pterodactylus sagittirostris. Fourteen species are considered valid, and diagnoses are provided to all of them: Ornithocheirus simus, Lonchodraco giganteus comb. n., Lonchodraco machaerorhynchus comb. n., Lonchodraco(?) microdon comb. n., Coloborhynchus clavirostris, ‘Ornithocheirus’ capito, Camposipterus nasutus comb. n., Camposipterus(?) sedgwickii comb. n., Camposipterus(?) colorhinus comb. n., Cimoliopterus cuvieri comb. n., ‘Ornithocheirus’ polyodon, ‘Ornithocheirus’ platystomus, ‘Pterodactylus’ daviesii, and ‘Ornithocheirus’ denticulatus. These species are referred in the genera Ornithocheirus, Lonchodraco gen. n., Coloborhynchus, Cimoliopterus gen. n., and Camposipterus gen. n., but additional genera are probably present, as indicated by the use of single quotation marks throughout the text. A cladistic analysis demonstrates that Anhangueridae lies within a newly recognized clade, here

What Belongs in Your 15-Bean Soup? Using the Learning Cycle to Address Misconceptions about Construction of Taxonomic Keys

ERIC Educational Resources Information Center

Ross, Ann; Vanderspool, Staria

2004-01-01

Students can use seed characteristics to discriminate between the different kinds of legumes using taxonomic classification processes of sorting and ranking, followed by construction of taxonomic keys. The application of the Learning Cycle process to taxonomic principles, hierarchical classification, and construction of keys presents the…

Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex.

PubMed

Campbell, Polly; Schneider, Christopher J; Adnan, Adura M; Zubaid, Akbar; Kunz, Thomas H

2004-12-01

Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

STARS experiential group intervention: a complex trauma treatment approach for survivors of human trafficking.

PubMed

Hopper, Elizabeth K; Azar, Naomi; Bhattacharyya, Sriya; Malebranche, Dominique A; Brennan, Kelsey E

2018-01-01

This is the abstract that was submitted online with the paper: Despite the fact that many survivors of human trafficking have experienced complex trauma, there are no established interventions designed to specifically address these impacts. Leaders in the field of complex trauma have advocated for the need for somatic approaches to intervention. This paper presents STARS Experiential Group treatment, the first structured bodybased group intervention that has been designed to address complex trauma in survivors of human trafficking. Three pilot groups were run in residential settings with adolescent and adult survivors of sex trafficking. Two adaptations were utilized, with one focusing on application of expressive arts modalities and the other incorporating theater games. Qualitative results, using thematic analysis, identified several themes related to challenges and potential benefits of these groups. Potential benefits of the STARS groups were found in the areas of Interpersonal Relationships, Regulation, and Self/ Identity, with fourteen sub-themes further describing positive impacts. Challenges within these areas are explored, to inform the development of group interventions for trafficking survivors. The results of this paper suggest that experiential, somatically-oriented group treatment shows promise as an important element of holistic intervention with trafficking survivors.

Cracking complex taxonomy of Costa Rican moths: Anacrusis Zeller (Lepidoptera: Tortricidae)

USDA-ARS?s Scientific Manuscript database

Remarkably similar forewing patterns, striking sexual dimorphism, and rampant sympatry all combine to present a taxonomically and morphologically bewildering complex of five species of Anacrusis tortricid moths in Central America: Anacrusis turrialbae Razowski, Anacrusis piriferana (Zeller), Anacrus...

A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae).

PubMed

Poe, Steven; Nieto-Montes de Oca, Adrián; Torres-Carvajal, Omar; De Queiroz, Kevin; Velasco, Julián A; Truett, Brad; Gray, Levi N; Ryan, Mason J; Köhler, Gunther; Ayala-Varela, Fernando; Latella, Ian

2017-09-01

Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A taxonomic synopsis of Altingiaceae with nine new combinations

PubMed Central

Ickert-Bond, Stefanie M.; Wen, Jun

2013-01-01

Abstract A taxonomic synopsis of the Altingiaceae is presented, including the taxonomic enumeration and distribution of 15 recognized species based on studies of 1,500 specimens from 24 herbaria throughout the distributional range of the taxa. Previous phylogenetic analyses based on several molecular markers have shown that Altingia and Semiliquidambar are nested within Liquidambar. All Altingia and Semiliquidambar species are now formally transferred to Liquidambar, which has the nomenclatural priority. The following nine new combinations are herein made: Liquidambar cambodiana(Lecomte) Ickert-Bond & J. Wen, Liquidambar caudata (H. T. Chang) Ickert-Bond & J. Wen, Liquidambar chingii (Metcalf) Ickert-Bond & J. Wen, Liquidambar gracilipes (Hemsl.) Ickert-Bond & J. Wen, Liquidambar multinervis(Cheng) Ickert-Bond & J. Wen, Liquidambar obovata (Merrill & Chun) Ickert-Bond & J. Wen, Liquidambar poilanei (Tardieu) Ickert-Bond & J. Wen, Liquidambar siamensis (Craib) Ickert-Bond & J. Wen, and Liquidambar yunnanensis (Rehder & Wilson) Ickert-Bond & J. Wen. PMID:24399902

Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests.

PubMed

Lamarre, Greg P A; Hérault, Bruno; Fine, Paul V A; Vedel, Vincent; Lupoli, Roland; Mesones, Italo; Baraloto, Christopher

2016-01-01

Arthropods represent most of global biodiversity, with the highest diversity found in tropical rain forests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass sampling of arthropod communities within three major habitat types of lowland Amazonian rain forest, including terra firme clay, white-sand and seasonally flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in the two regions. The overall arthropod community composition exhibited strong turnover among habitats and between regions. In particular, seasonally flooded forest habitats of both regions comprised unique assemblages. Overall, 17·7% (26 of 147) of arthropod families showed significant preferences for a particular habitat type. We present a first reproducible arthropod functional classification among the 147 taxa based on similarity among 21 functional traits describing feeding source, major mouthparts and microhabitats inhabited by each taxon. We identified seven distinct functional groups whose relative abundance contrasted strongly across the three habitats, with sap and leaf feeders showing higher abundances in terra firme clay forest. Our novel arthropod functional classification provides an important complement to link these contrasting patterns of composition to differences in forest functioning across geographical and environmental gradients. This study underlines that both environment and biogeographical processes are responsible for driving arthropod taxonomic composition while environmental filtering is the main driver of the variance in functional composition. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Taxonomic composition and biostratigraphic value of the Early Riphean organic-walled microfossil association from the Ust'-Il'ya Formation of the Anabar Uplift, Northern Siberia

NASA Astrophysics Data System (ADS)

Sergeev, V. N.; Vorob'eva, N. G.; Petrov, P. Yu.; Semikhatov, M. A.

2017-05-01

It is demonstrated on the basis of the first monographic study of multiple and taxonomically variable organic-walled microfossils from the Ust'-Il'ya Formation of the Anabar Uplift that both prokaryotic and eukaryotic forms are present in the composition of this microbiota. They are divided into four formal groups on the basis of the specifics of the morphological indicators of the identified taxa. The review of the data on the isotopic age of hosting deposits showed that the Ust'-Il'ya Formation is of the Early Riphean in age which are currently evaluated as 1750 ± 10-1400 Ma. Relatively large and morphologically complex eukaryotic forms present in the Ust'-Il'ya Formation served in due time as the basis for an erroneous conclusion on the Late Riphean age of the specified formation and the overlying Lower Kotuikan Subformation of the Anabar Uplift. The paper provides a global comparative analysis of the Early Riphean microbiotas, demonstrates the position of the Ust'-Il'ya and Kotuikan microbiotas amidst the microbiotas of the same age, and shows that the relatively large acanthomorphic acritarchs Tappania, Valeria, Dictiosphaera, Satka, and Shuiyousphaeridium appeared in the geological history already during the Early Riphean Erathem. Moreover, the paper discusses the recently published data on the distribution of aerobic and anaerobic conditions in the Early Riphean paleobasins and provides the conclusion on the impact of the lateral change of these conditions on the taxonomic composition of the microbiota.

Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

PubMed

Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

2008-07-07

Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

Phylogenetics of the phlebotomine sand fly group Verrucarum (Diptera: Psychodidae: Lutzomyia).

PubMed

Cohnstaedt, Lee W; Beati, Lorenza; Caceres, Abraham G; Ferro, Cristina; Munstermann, Leonard E

2011-06-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity--the Lutzomyia longiflocosa-Lutzomyia sauroida pair and the Lutzomyia quasitownsendi-Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution.

Phylogenetics of the Phlebotomine Sand Fly Group Verrucarum (Diptera: Psychodidae: Lutzomyia)

PubMed Central

Cohnstaedt, Lee W.; Beati, Lorenza; Caceres, Abraham G.; Ferro, Cristina; Munstermann, Leonard E.

2011-01-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity—the Lutzomyia longiflocosa–Lutzomyia sauroida pair and the Lutzomyia quasitownsendi–Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution. PMID:21633028

Rotational Study of Ambiguous Taxonomic Classified Asteroids

NASA Astrophysics Data System (ADS)

Linder, Tyler R.; Sanchez, Rick; Wuerker, Wolfgang; Clayson, Timothy; Giles, Tucker

2017-01-01

The Sloan Digital Sky Survey (SDSS) moving object catalog (MOC4) provided the largest ever catalog of asteroid spectrophotometry observations. Carvano et al. (2010), while analyzing MOC4, discovered that individual observations of asteroids which were observed multiple times did not classify into the same photometric-based taxonomic class. A small subset of those asteroids were classified as having both the presence and absence of a 1um silicate absorption feature. If these variations are linked to differences in surface mineralogy, the prevailing assumption that an asteroid’s surface composition is predominantly homogenous would need to be reexamined. Furthermore, our understanding of the evolution of the asteroid belt, as well as the linkage between certain asteroids and meteorite types may need to be modified.This research is an investigation to determine the rotational rates of these taxonomically ambiguous asteroids. Initial questions to be answered:Do these asteroids have unique or nonstandard rotational rates?Is there any evidence in their light curve to suggest an abnormality?Observations were taken using PROMPT6 a 0.41-m telescope apart of the SKYNET network at Cerro Tololo Inter-American Observatory (CTIO). Observations were calibrated and analyzed using Canopus software. Initial results will be presented at AAS.

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

PubMed

Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

2017-10-01

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

Habitat connectivity and local conditions shape taxonomic and functional diversity of arthropods on green roofs.

PubMed

Braaker, Sonja; Obrist, Martin Karl; Ghazoul, Jaboury; Moretti, Marco

2017-05-01

Increasing development of urban environments creates high pressure on green spaces with potential negative impacts on biodiversity and ecosystem services. There is growing evidence that green roofs - rooftops covered with vegetation - can contribute mitigate the loss of urban green spaces by providing new habitats for numerous arthropod species. Whether green roofs can contribute to enhance taxonomic and functional diversity and increase connectivity across urbanized areas remains, however, largely unknown. Furthermore, only limited information is available on how environmental conditions shape green roof arthropod communities. We investigated the community composition of arthropods (Apidae, Curculionidae, Araneae and Carabidae) on 40 green roofs and 40 green sites at ground level in the city of Zurich, Switzerland. We assessed how the site's environmental variables (such as area, height, vegetation, substrate and connectivity among sites) affect species richness and functional diversity using generalized linear models. We used an extension of co-inertia analysis (RLQ) and fourth-corner analysis to highlight the mechanism underlying community assemblages across taxonomic groups on green roof and ground communities. Species richness was higher at ground-level sites, while no difference in functional diversity was found between green roofs and ground sites. Green roof arthropod diversity increased with higher connectivity and plant species richness, irrespective of substrate depth, height and area of green roofs. The species trait analysis reviewed the mechanisms related to the environmental predictors that shape the species assemblages of the different taxa at ground and roof sites. Our study shows the important contribution of green roofs in maintaining high functional diversity of arthropod communities across different taxonomic groups, despite their lower species richness compared with ground sites. Species communities on green roofs revealed to be characterized

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

2015-01-01

Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

PubMed Central

Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

2016-01-01

We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

PubMed Central

Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

2015-01-01

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

Small-Group Problem-Based Learning as a Complex Adaptive System

ERIC Educational Resources Information Center

Mennin, Stewart

2007-01-01

Small-group problem-based learning (PBL) is widely embraced as a method of study in health professions schools and at many different levels of education. Complexity science provides a different lens with which to view and understand the application of this method. It presents new concepts and vocabulary that may be unfamiliar to practitioners of…

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

PubMed

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

PubMed Central

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

A Complex Systems Investigation of Group Work Dynamics in L2 Interactive Tasks

ERIC Educational Resources Information Center

Poupore, Glen

2018-01-01

Working with Korean university-level learners of English, this study provides a detailed analytical comparison of 2 task work groups that were video-recorded, with 1 group scoring very high and the other relatively low based on the results of a Group Work Dynamic (GWD) measuring instrument. Adopting a complexity theory (CT) perspective and…

Colobopsis explodens sp. n., model species for studies on "exploding ants" (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group.

PubMed

Laciny, Alice; Zettel, Herbert; Kopchinskiy, Alexey; Pretzer, Carina; Pal, Anna; Salim, Kamariah Abu; Rahimi, Mohammad Javad; Hoenigsberger, Michaela; Lim, Linda; Jaitrong, Weeyawat; Druzhinina, Irina S

2018-01-01

A taxonomic description of all castes of Colobopsis explodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on "exploding ants" in Southeast Asia. The new species is a member of the Colobopsis cylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsis saundersi (Emery, 1889) (formerly Camponotus saundersi ). The COCY species group is known under its vernacular name "exploding ants" for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsis explodens Laciny & Zettel, sp. n. and Colobopsis badia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C. explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C. badia , a lectotype from Singapore is designated. The following taxonomic changes within the C. saundersi complex are proposed: Colobopsis solenobia (Menozzi, 1926), syn. n. and Colobopsis trieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsis corallina Roger, 1863, a common endemic species of the Philippines. Colobopsis saginata Stitz, 1925, stat. n ., hitherto a subspecies of C. badia , is raised to species level.

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

PubMed

Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

2015-10-01

The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

Separation of compounds with multiple -OH groups from dilute aqueous solutions via complexation with organoboronate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chow, Tina Kuo Fung

1992-05-01

The complexing extractant agent investigated in this work is 3-nitrophenylboronic acid (NPBA) in its anionic form (NPB). NPBA and Aliquat 336 (quaternary amine) is dissolved in 2-ethyl-l-hexanol, and the extractant is contacted with aq. NaOH. Solutes investigated were 1,2-propanediol, glycerol, fructose, sorbitol and lactic acid. Batch extraction experiments were performed at 25°C. Partition coefficients, distribution ratios and loadings are reported for varying concentrations of solute and NPB. All solutes complexed with NPB -, with all complexes containing only one NPB - per complex. The 1:1 complexation constants for the solutes glycerol, fructose and sorbitol follow trends similar to complexation withmore » B(OH) 4 - (aq.), i.e. the complexation constants increase with increasing number of -OH groups available for complexation. Assumption of 1:1 complex is not valid for 1, 2-propanediol, which showed overloading (more than one mole of solute complexed to one mole NPB -) at higher concentrations. The -OH group on the NPB - which is left uncomplexed after one solute molecule had bound to the other two -OH groups may be responsible for the overloading. Overloading is also observed in extraction of tactic acid, but through a different mechanism. It was found that TOMA + can extract lactic acid to an extent comparable to the uptake of lactic acid by NPB -. The complexation is probably through formation of an acid-base ion pair. Losses of NPBA into the aqueous phase could lead to problems, poor economics in industrial separation processes. One way of overcoming this problem would be to incorporate the NPBA onto a solid support.« less

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

PubMed

Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further

Positional effects of hydroxy groups on catalytic activity of proton-responsive half-sandwich Cp*Iridium(III) complexes

DOE PAGES

Suna, Yuki; Fujita, Etsuko; Ertem, Mehmed Z.; ...

2014-11-12

Proton-responsive half-sandwich Cp*Ir(III) complexes possessing a bipyridine ligand with two hydroxy groups at the 3,3'-, 4,4'-, 5,5'- or 6,6'-positions (3DHBP, 4DHBP, 5DHBP, or 6DHBP) were systematically investigated. UV-vis titration data provided average pK a values of the hydroxy groups on the ligands. Both hydroxy groups were found to deprotonate in the pH 4.6–5.6 range for the 4–6DHBP complexes. One of the hydroxy groups of the 3DHBP complex exhibited the low pK a value of < 0.4 because the deprotonation is facilitated by the strong intramolecular hydrogen bond formed between the generated oxyanion and the remaining hydroxy group, which in turnmore » leads to an elevated pK a value of ~13.6 for the second deprotonation step. The crystal structures of the 4– and 6DHBP complexes obtained from basic aqueous solutions revealed their deprotonated forms. The intramolecular hydrogen bond in the 3DHBP complex was also observed in the crystal structures. The catalytic activities of these complexes in aqueous phase reactions, at appropriate pH, for hydrogenation of carbon dioxide (pH 8.5), dehydrogenation of formic acid (pH 1.8), transfer hydrogenation reactions using formic acid/formate as a hydrogen source (pH 7.2 and 2.6) were investigated to compare the positional effects of the hydroxy groups. The 4– and 6DHBP complexes exhibited remarkably enhanced catalytic activities under basic conditions because of the resonance effect of the strong electrondonating oxyanions, whereas the 5DHBP complex exhibited negligible activity despite the presence of electron-donating groups. The 3DHBP complex exhibited relatively high catalytic activity at low pH owing to the one strong electron-donating oxyanion group stabilized by the intramolecular hydrogen bond. DFT calculations were employed to study the mechanism of CO₂ hydrogenation by the 4DHBP and 6DHBP complexes, and comparison of the activation free energies of the H₂ heterolysis and CO₂ insertion steps

A "taxonomic affidavit": Why it is needed?

PubMed

Por, Francis Dov

2007-06-01

Imprecise and faulty taxonomic identification of the biological objects of many ecological and experimental studies renders these studies irreproducible. Incomplete identification to the species level and excessive use of vernacular species names are additional problems. Good science must be able to be falsified. I recommend that publications and granting agencies use and mention the names of the zoologists or botanists who identified the species. Voucher specimens should be marked and deposited in scientific museums for future checking.

Focused Research Group in Correlated Electron and Complex Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ziqiang

While the remarkable physical properties of correlated and complex electronic materials hold great promise for technological applications, one of the key values of the research in this field is its profound impact on fundamental physics. The transition metal oxides, pnictides, and chalcogenides play a key role and occupy an especially important place in this field. The basic reason is that the outer shell of transition metals contains the atomic d-orbitals that have small spatial extent, but not too small to behave as localized orbtials. These d-electrons therefore have a small wave function overlap in a solid, e.g. in an octahedralmore » environment, and form energy bands that are relatively narrow and on the scale of the short-range intra-atomic Coulomb repulsion (Hubbard U). In this intermediate correlation regime lies the challenge of the many-body physics responsible for new and unconventional physical properties. The study of correlated electron and complex materials represents both the challenge and the vitality of condensed matter and materials physics and often demands close collaborations among theoretical and experimental groups with complementary techniques. Our team has a track record and a long-term research goal of studying the unusual complexities and emergent behaviors in the charge, spin, and orbital sectors of the transition metal compounds in order to gain basic knowledge of the quantum electronic states of matter. During the funding period of this grant, the team continued their close collaborations between theory, angle-resolved photoemission spectroscopy, and scanning tunneling microscopy and made significant progress and contributions to the field of iron-based superconductors, copper-oxide high-temperature superconductors, triangular lattice transition metal oxide cobaltates, strontium ruthenates, spin orbital coupled iridates, as well as topological insulators and other topological quantum states of matter. These results include both new

Structure of a group II intron in complex with its reverse transcriptase.

PubMed

Qu, Guosheng; Kaushal, Prem Singh; Wang, Jia; Shigematsu, Hideki; Piazza, Carol Lyn; Agrawal, Rajendra Kumar; Belfort, Marlene; Wang, Hong-Wei

2016-06-01

Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.

Taxonomic relationships among Phenacomys voles as inferred by cytochrome b.

Treesearch

M. Renee Bellinger; Susan M. Haig; Eric D. Forsmann; Thomas D. Mullins

2005-01-01

Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. I. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial...

Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

PubMed Central

Laciny, Alice; Zettel, Herbert; Kopchinskiy, Alexey; Pretzer, Carina; Pal, Anna; Salim, Kamariah Abu; Rahimi, Mohammad Javad; Hoenigsberger, Michaela; Lim, Linda; Jaitrong, Weeyawat; Druzhinina, Irina S.

2018-01-01

Abstract A taxonomic description of all castes of Colobopsis explodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsis cylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsis saundersi (Emery, 1889) (formerly Camponotus saundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsis explodens Laciny & Zettel, sp. n. and Colobopsis badia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C. explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C. badia, a lectotype from Singapore is designated. The following taxonomic changes within the C. saundersi complex are proposed: Colobopsis solenobia (Menozzi, 1926), syn. n. and Colobopsis trieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsis corallina Roger, 1863, a common endemic species of the Philippines. Colobopsis saginata Stitz, 1925, stat. n., hitherto a subspecies of C. badia, is raised to species level. PMID:29706783

Complex reflection groups, logarithmic connections and bi-flat F-manifolds

NASA Astrophysics Data System (ADS)

Arsie, Alessandro; Lorenzoni, Paolo

2017-10-01

We show that bi-flat F-manifolds can be interpreted as natural geometrical structures encoding the almost duality for Frobenius manifolds without metric. Using this framework, we extend Dubrovin's duality between orbit spaces of Coxeter groups and Veselov's ěe -systems, to the orbit spaces of exceptional well-generated complex reflection groups of rank 2 and 3. On the Veselov's ěe -systems side, we provide a generalization of the notion of ěe -systems that gives rise to a dual connection which coincides with a Dunkl-Kohno-type connection associated with such groups. In particular, this allows us to treat on the same ground several different examples including Coxeter and Shephard groups. Remarkably, as a by-product of our results, we prove that in some examples, basic flat invariants are not uniquely defined. As far as we know, such a phenomenon has never been pointed out before.

Group Planning and Task Efficiency with Complex Problems. Final Report.

ERIC Educational Resources Information Center

Lawson, E. D.

One hundred eighty 4-man groups (90 of men and 90 of women) using 3 types of net (All-Channel, Wheel and Circle) under 3 conditions (Planning Period (PP), Rest Period (RP) and Control) were run in a single session with 5 complex problems to determine whether a single 2-minute planning period after solution of the first problem would result in…

The integripennis species group of Geocharidius Jeannel, 1963 (Carabidae, Bembidiini, Anillina) from Nuclear Central America: a taxonomic review with notes about biogeography and speciation

PubMed Central

Sokolov, Igor M.; Kavanaugh, David H.

2014-01-01

Abstract Our review recognizes 15 species of the integripennis species group of Geocharidius from Nuclear Central America, include three species previously described (Geocharidius gimlii Erwin, Geocharidius integripennis (Bates) and Geocharidius zullinii Vigna Taglianti) and 12 described here as new. They are: Geocharidius andersoni sp. n. (type locality: Chiapas, Chiapas Highlands, Cerro Huitepec) and Geocharidius vignatagliantii sp. n. (type locality: Chiapas, Motozintla, Sierra Madre de Chiapas, Benito Juárez) from Mexico; Geocharidius antigua sp. n. (type locality: Sacatepéquez, 5 km SE of Antigua), Geocharidius balini sp. n. (type locality: Suchitepéquez, 4 km S of Volcan Atitlán), Geocharidius erwini sp. n. (type locality: Quiché Department, 7 km NE of Los Encuentros), Geocharidius jalapensis sp. n. (type locality: Jalapa Department, 4 km E of Mataquescuintla), Geocharidius longinoi, sp. n. (type locality: El Progreso Department, Cerro Pinalón), and Geocharidius minimus sp. n. (type locality: Sacatepéquez Department, 5 km SE of Antigua) from Guatemala; and Geocharidius celaquensis sp. n. (type locality: Lempira Department, Celaque National Park), Geocharidius comayaguanus sp. n. (type locality: Comayagua Department, 18 km ENE of Comayagua), Geocharidius disjunctus sp. n. (type locality: Francisco Morazán, La Tigra National Park), and Geocharidius lencanus sp. n. (type locality: Lempira Department, Celaque National Park) from Honduras. For all members of the group, adult structural characters, including male and female genitalia, are described, and a taxonomic key for all members of the integripennis species group is presented based on these characters. Behavioral and biogeographical aspects of speciation in the group are discussed, based on the morphological analysis. In all cases of sympatry, pairs of closely related species show greater differences in sizes than pairs of more remotely related species. Integripennis group species occupy six different

Taxonomic Knowledge of Children with and without Cochlear Implants

ERIC Educational Resources Information Center

Lund, Emily; Dinsmoor, Jessica

2016-01-01

Purpose: The purpose of this study was to compare the taxonomic vocabulary knowledge and organization of children with cochlear implants to (a) children with normal hearing matched for age, and (b) children matched for vocabulary development. Method: Ten children with cochlear implants, 10 age-matched children with normal hearing, and 10…

Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

PubMed

Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

2013-01-01

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history.

PubMed

Berke, Lidija; Snel, Berend

2015-03-13

Polycomb repressive complex 1 (PRC1) is an essential protein complex for plant development. It catalyzes ubiquitination of histone H2A that is an important part of the transcription repression machinery. Absence of PRC1 subunits in Arabidopsis thaliana plants causes severe developmental defects. Many aspects of the plant PRC1 are elusive, including its origin and phylogenetic distribution. We established the evolutionary history of the plant PRC1 subunits (LHP1, Ring1a-b, Bmi1a-c, EMF1, and VRN1), enabled by sensitive phylogenetic methods and newly sequenced plant genomes from previously unsampled taxonomic groups. We showed that all PRC1 core subunits exist in gymnosperms, earlier than previously thought, and that VRN1 is a recent addition, found exclusively in eudicots. The retention of individual subunits in chlorophytes, mosses, lycophytes and monilophytes indicates that they can moonlight as part of other complexes or processes. Moreover, we showed that most PRC1 subunits underwent a complex, duplication-rich history that differs significantly between Brassicaceae and other eudicots. PRC1 existed in the last common ancestor of seed plants where it likely played an important regulatory role, aiding their radiation. The presence of LHP1, Ring1 and Bmi1 in mosses, lycophytes and monilophytes also suggests the presence of a primitive yet functional PRC1.

Taxonomic and thematic organisation of proper name conceptual knowledge.

PubMed

Crutch, Sebastian J; Warrington, Elizabeth K

2011-01-01

We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g., action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g., Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation - taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g., Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g., Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g., Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle.

Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

PubMed Central

Crutch, Sebastian J.; Warrington, Elizabeth K.

2011-01-01

We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g. action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g. Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation – taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g. Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g. Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g. Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle. PMID:22063815

Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

PubMed

Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S

2015-01-01

Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the "survey and manage" provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrusgreggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrusgreggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrusgreggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7-12.1%). Additionally we found that the Columbia duskysnail and Colligyrusgreggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrusgreggi.

Phylogenetic relationships of leopard frogs (Rana pipiens complex) from an isolated coastal mountain range in southern Sonora, Mexico.

PubMed

Pfeiler, E; Markow, T A

2008-10-01

Mitochondrial DNA sequence data from the control region and 12S rRNA in leopard frogs from the Sierra El Aguaje of southern Sonora, Mexico, together with GenBank sequences, were used to infer taxonomic identity and provide phylogenetic hypotheses for relationships with other members of the Rana pipiens complex. We show that frogs from the Sierra El Aguaje belong to the Rana berlandieri subgroup, or Scurrilirana clade, of the R. pipiens group, and are most closely related to Rana magnaocularis from Nayarit, Mexico. We also provide further evidence that Rana magnaocularis and R. yavapaiensis are close relatives.

Evolution of cooperation on complex networks with synergistic and discounted group interactions

NASA Astrophysics Data System (ADS)

Zhou, Lei; Li, Aming; Wang, Long

2015-06-01

In the real world individuals often engage in group interactions and their payoffs are determined by many factors, including the typical nonlinear interactions, i.e., synergy and discounting. Previous literatures assume that individual payoffs are either synergistically enhanced or discounted with the additional cooperators. Such settings ignore the interplay of these two factors, which is in sharp contrast with the fact that they ubiquitously coexist. Here we investigate how the coexistence and periodical switching of synergistic and discounted group interactions affect the evolution of cooperation on various complex networks. We show that scale-free networks facilitate the emergence of cooperation in terms of fixation probability for group interactions. With nonlinear interactions the heterogeneity of the degree acts as a double-edged sword: below the neutral drift it is the best for cooperation while above the neutral drift it instead provides the least opportunity for cooperators to be fixed. The advantages of the heterogeneity fade as interactive attributes switch between synergy and discounting, which suggests that the heterogeneity of population structures cannot favor cooperators in group interactions even with simple nonlinear interactions. Nonetheless, scale-free networks always guarantee cooperators the fastest rate of fixation. Our work implies that even very simple nonlinear group interactions could greatly shape the fixation probability and fixation time of cooperators in structured populations indicated by complex networks.

Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

PubMed

Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

2016-04-01

This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Distribution of taxonomic classes and the compositional structure of the asteroid belt

NASA Technical Reports Server (NTRS)

Gradie, Jonathan C.; Chapman, Clark R.; Tedesco, Edward F.

1989-01-01

This paper reviews previous studies on the distribution of the asteroid taxonomic classes and analyzes the techniques, results, and interpretations of these studies, with special attention given to the strong and weak points of these studies and the important caveat for their interpretation. It is concluded that, in spite of the differences in class definition, the rather ordered heliocentric distribution of the composition is real and must be due to either primordial, evolutionary, or dynamical processes, or to a combination of all three. In general, the distribution of asteroid taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner asteroid belt, and low-albedo asteroids prevalent in the outer belt and beyond.

[Taxonomic characteristics and mixed communities of wound infection agents in patients of reanimation and surgical departments of a hospital].

PubMed

Men'shikova, E D; Kiselevskaia-Babinina, I V; Men'shikov, D D; Godkov, M A

2012-01-01

Study of taxonomical structure ofwound infection agents, prevalence of mixes, and detection of character of their possible connection with the results of various microorganisms population interaction in septic wounds. A microbiological study of material from patients with wound infection (WI), 582 of those were cured in reanimation and intensive therapy departments (RITD; group 1) and 1455 - in surgical departments (SD; group 2), was performed. Taxonomic membership and ability to coexist was determined in 4129 microorganisms strains. Etiological role of the agents was evaluated by using values of consistency rate (CR). Species that were present in more than 50% of samples were considered consistent, in 25 to 50%--additional, and in less than 25%--random. Frequency rates (FR) were also determined, that is the fraction of a certain species (genus) of the microorganism (in %) from all the isolated cultures that correspond to 100%. For the determination of the significance of individual species of the agent in the structure of mixed microorganism populations, FR - their fraction (%) in mixed population from the number of strains of this species that correspond to 100% - was calculated. A significant part of the microorganisms strains, more frequently in reanimation department (65.5%), caused wound suppuration in populations mixed with other species of the agents. In reanimation and surgical departments consistent species of wound infection agents were not detected. A leading etiological role of Staphylococcus aureus (FR 19.2% and 23.9%) was determined, and FR of S. aureus strains in mixes was 64.6% in RITD and 46.8% in SD. The parameters ofotheragents of WI in the comparison groups were similar. However FR among mixes in RITD were significantly higher for streptococci that do not belong to S. pyogenes species (72,5%), and also nonfermentative microorganisms (67,2%), and in SD - in Klebsiella pneumoniae mixes. For agents of wound infection especially in RITD, low

Characteristic effects of substituent and external pressure on group-inclusion complexation with p-sulfonatocalix[8]arene and γ-cyclodextrin

NASA Astrophysics Data System (ADS)

Miyazono, Keitaro; Hanaya, Tadashi; Sueishi, Yoshimi

2014-07-01

By synthesizing unique nitroxide probes (α-substituted phenyl-2,4,6-trimethoxybenzyl(t-butyl)nitroxide), we have shown that p-sulfonatocalix[8]arene (Calix-S8) and γ-cyclodextin (γ-CD) form electron spin resonance spectroscopically separable group-inclusion complexes (α-substituted phenyl-in (R-in) and t-butyl-in complexes) and determined the group-inclusion constants of Calix-S8 and γ-CD. Using nitroxide probes, we have examined the effects of substituent and external pressure on group-inclusion complexation with Calix-S8 and γ-CD. Experiments on pressure dependence enabled us to calculate the reaction volume (Δ V) for R-in and t-butyl-in complex formations. Δ V for group-in complexation with Calix-S8 had negative values. In contrast, Δ V values for γ-CD showed positive values, which is responsible for the repelled water molecules in the CD cavity. The characteristic pressure effects on group-in complexation suggest that group recognition by γ-CD is sensitive when compared with that by Calix-S8.

Syntactical Complexity and Vocabulary Diversity in Two Groups of Children's Books.

ERIC Educational Resources Information Center

McCormick, Sandra

This study compared syntactic complexity and vocabulary diversity in two groups of books that can be used for reading aloud to preschool children: books recommended by authorities in reading and children's literature for reading aloud and "grocery store" books (small, inexpensive picture books that can be purchased in grocery stores). Trade names…

Reconstruction of Complex Directional Networks with Group Lasso Nonlinear Conditional Granger Causality.

PubMed

Yang, Guanxue; Wang, Lin; Wang, Xiaofan

2017-06-07

Reconstruction of networks underlying complex systems is one of the most crucial problems in many areas of engineering and science. In this paper, rather than identifying parameters of complex systems governed by pre-defined models or taking some polynomial and rational functions as a prior information for subsequent model selection, we put forward a general framework for nonlinear causal network reconstruction from time-series with limited observations. With obtaining multi-source datasets based on the data-fusion strategy, we propose a novel method to handle nonlinearity and directionality of complex networked systems, namely group lasso nonlinear conditional granger causality. Specially, our method can exploit different sets of radial basis functions to approximate the nonlinear interactions between each pair of nodes and integrate sparsity into grouped variables selection. The performance characteristic of our approach is firstly assessed with two types of simulated datasets from nonlinear vector autoregressive model and nonlinear dynamic models, and then verified based on the benchmark datasets from DREAM3 Challenge4. Effects of data size and noise intensity are also discussed. All of the results demonstrate that the proposed method performs better in terms of higher area under precision-recall curve.

Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups.

PubMed

Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives I Batlle, Jordi; Oughton, Deborah H; Garnier-Laplace, Jacqueline

2016-02-01

soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 μGy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 μGy h(-1) in mammals to 970 μGy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices

NASA Astrophysics Data System (ADS)

White, J. C.; Hill, M. J.; Bickerton, M. A.; Wood, P. J.

2017-09-01

The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.

Toward an accurate taxonomic interpretation of Carex fossil fruits (Cyperaceae): a case study in section Phacocystis in the Western Palearctic.

PubMed

Jiménez-Mejías, Pedro; Martinetto, Edoardo

2013-08-01

Despite growing interest in the systematics and evolution of the hyperdiverse genus Carex, few studies have focused on its evolution using an absolute time framework. This is partly due to the limited knowledge of the fossil record. However, Carex fruits are not rare in certain sediments. We analyzed carpological features of modern materials from Carex sect. Phacocystis to characterize the fossil record taxonomically. We studied 374 achenes from modern materials (18 extant species), as well as representatives from related groups, to establish the main traits within and among species. We also studied 99 achenes from sediments of living populations to assess their modification process after decay. Additionally, we characterized 145 fossil achenes from 10 different locations (from 4-0.02 mya), whose taxonomic assignment we discuss. Five main characters were identified for establishing morphological groups of species (epidermis morphology, achene-utricle attachment, achene base, style robustness, and pericarp section). Eleven additional characters allowed the discrimination at species level of most of the taxa. Fossil samples were assigned to two extant species and one unknown, possibly extinct species. The analysis of fruit characters allows the distinction of groups, even up to species level. Carpology is revealed as an accurate tool in Carex paleotaxonomy, which could allow the characterization of Carex fossil fruits and assign them to subgeneric or sectional categories, or to certain species. Our conclusions could be crucial for including a temporal framework in the study of the evolution of Carex.

Synthesis, structure and DFT study of cymantrenyl Fischer carbene complexes of group VI and VII transition metals

NASA Astrophysics Data System (ADS)

Fraser, Roan; van Rooyen, Petrus H.; Landman, Marilé

2016-02-01

Bi- and trimetallic carbene complexes of group VI and VII transition metals (Cr, Mo, W, Mn and Re), with CpMn(CO)3 as the initial synthon, have been synthesised according to the classical Fischer methodology. Crystal structures of the novel carbene complexes with general formula [Mx(CO)y-1{C(OEt)(MnCp(CO)3)}], where x = 1 then y = 3 or 6; x = 2 then y = 10, of the complexes are reported. A density functional theory (DFT) study was undertaken to determine natural bonding orbitals (NBOs) and conformational as well as isomeric aspects of the polymetallic complexes. Application of the second-order perturbation theory (SOPT) of the natural bond orbital (NBO) method revealed stabilizing interactions between the methylene C-H bonds and the carbonyl ligands of the carbene metal moiety. These stabilization interactions show a linear decrease for the group VI metal carbene complexes down the group.

fac-Re(CO)3L complexes containing tridentate monoanionic ligands (L-) with a seldom-studied sulfonamido group as one terminal ligating group.

PubMed

Christoforou, Anna Maria; Fronczek, Frank R; Marzilli, Patricia A; Marzilli, Luigi G

2007-08-20

To achieve a net-neutral coordination unit in radiopharmaceuticals with a fac-M(CO)3+ core (M = Tc, Re), facially coordinated monoanionic tridentate ligands are needed. New neutral fac-Re(CO)3L complexes were obtained by treating fac-[Re(CO)3(H2O)3]+ with unsymmetrical tridentate NNN donor ligands (LH) based primarily on a diethylenetriamine (dien) moiety with an aromatic group linked to a terminal nitrogen through a sulfonamide. LHs contain 2,4,6-trimethylbenzenesulfonyl (tmbSO2) and 5-(dimethylamino)naphthalene-1-sulfonyl (DNS) groups. X-ray crystallographic and NMR analyses confirm that in both the solid and the solution states all L- in fac-Re(CO)3L complexes are bound in a tridentate fashion with one donor being nitrogen from a deprotonated sulfonamido group. Another fundamental property that is important in radiopharmaceuticals is shape, which in turn depends on ring pucker. For L- = tmbSO2-dien-, tmbSO2-N'-Medien-, and tmbSO2-N,N-Me2dien-, the two chelate rings have a different pucker chirality, as is commonly found for a broad range of metal complexes. However, for fac-Re(CO)3(DNS-dien), both chelate rings have the same pucker chirality because the sulfonamido ring has an unusual pucker for the absolute configuration at Re; a finding that is attributable to intramolecular and intermolecular hydrogen bonds from the sulfonamido oxygens to the NH2 groups. Averaging of tmb NMR signals, even at -90 degrees C for Re(CO)3(tmbSO2-N,N-Me2dien), indicates rapid dynamic motion in the complexes with this group. However, examination of the structures suggests that free rotation about the S-C(tmb) bond is not possible but that concerted coupled rotations about the N-S and the S-C bonds can explain the NMR data.

Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

PubMed Central

Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

2013-01-01

In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID

Complex within complex: integrative taxonomy reveals hidden diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and unexpected relationships with a song divergent relative

USDA-ARS?s Scientific Manuscript database

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premati...

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing.

PubMed

Endara, Lorena; Cui, Hong; Burleigh, J Gordon

2018-03-01

Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.

Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence.

PubMed

Cacciali, Pier; KÖhler, Gunther

2018-01-25

Tropidurus is a Neotropical genus of iguanoid lizards characterized by a conspicuously enlarged interparietal plate, the presence of gular folds, presence of infradigital keels, and the absence of femoral pores. Currently, 29 species are recognized within the genus, seven of which are present in Paraguay: T. etheridgei, T. torquatus, T. guarani, T. lagunablanca, T. spinulosus, T. tarara, and T. teyumirim. We generated genetic data based on two DNA mitochondrial markers (16S and COI) and one nuclear (PRLR) marker for all the seven Paraguayan species with the goal to identify the taxonomic relationships among taxa based on the intra- and interspecific genetic variation and the construction of molecular clusters. ML and BI analyses match in the recognition of two main clusters: groups torquatus and spinulosus, and within the torquatus group the differentiation between T. catalanensis and T. etheridgei is highly supported. Nevertheless, there is a complete lack of congruence between mitochondrial and nuclear genes in the topology within the spinulosus group. Tropidurus guarani and T. spinulosus are more differentiated from the remaining species of the spinulosus group with genetic p-distances from 4.0 to 6.0. Low distances were found between T. lagunablanca and T. tarara (1.0-1.1%), and slightly higher, among T. teyumirim, T. lagunablanca, and T. tarara (2.0-2.6% respectively). From a morphological perspective, species of the Tropidurus torquatus group are easily distinguished; but we found strong overlaps of scalation characters in the spinulosus group. We interpret the low genetic distances documented among the nominal taxa Tropidurus lagunablanca, T. tarara, and T. teyumirim as evidence for conspecificity. This hypothesis is supported by the lack of morphological characters that would diagnose any of the three taxa. Similarly, we found low genetic distances among populations assigned to the nominal taxa T. guarani and T. spinulosus, including samples from near the

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

PubMed Central

Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci

USGS Publications Warehouse

Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

Taxonomic status of Myotis occultus

USGS Publications Warehouse

Valdez, E.W.; Choate, Jerry R.; Bogan, M.A.; Yates, Terry L.

1999-01-01

The taxonomic status of the Arizona myotis (Myotis occultus) is uncertain. Although the taxon was described as a distinct species and currently is regarded as such by some authors, others have noted what they interpreted as intergradation with the little brown bat (M. lucifugus carissima) near the Colorado-New Mexico state line. In this study, we used protein electrophoresis to compare bats of these nominal taxa. We examined 20 loci from 142 specimens referable to M. occultus and M. lucifugus from New Mexico, Colorado, and Wyoming. Nine of the 20 loci were polymorphic. Results show that there were high similarities among samples, no fixed alleles, and minor divergence from Hardy-Weinberg equilibrium. Our results suggest that the two nominal taxa represent only one species and that M. occultus should be regarded as a subspecies of M. lucifugus.

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

An Exploratory Framework for Handling the Complexity of Mathematical Problem Posing in Small Groups

ERIC Educational Resources Information Center

Kontorovich, Igor; Koichu, Boris; Leikin, Roza; Berman, Avi

2012-01-01

The paper introduces an exploratory framework for handling the complexity of students' mathematical problem posing in small groups. The framework integrates four facets known from past research: task organization, students' knowledge base, problem-posing heuristics and schemes, and group dynamics and interactions. In addition, it contains a new…

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Researchers and stakeholders shape advances in management of tree and vine trunk-disease complexes

USDA-ARS?s Scientific Manuscript database

The grapevine trunk-disease complex limits grape production and vineyard longevity worldwide. Every vineyard in California eventually is infected by one or more trunk diseases. The causal fungi, which are taxonomically unrelated Ascomycetes, infect and then degrade the permanent woody structure of t...

Comparative SEM and LM foliar epidermal and palyno-morphological studies of Amaranthaceae and its taxonomic implications.

PubMed

Hussain, Amara Noor; Zafar, Muhammad; Ahmad, Mushtaq; Khan, Raees; Yaseen, Ghulam; Khan, Muhammad Saleem; Nazir, Abdul; Khan, Amir Muhammad; Shaheen, Shabnum

2018-05-01

Palynological features as well as comparative foliar epidermal using light and scanning electron microscope (SEM) of 17 species (10genera) of Amaranthaceae have been studied for its taxonomic significance. Different foliar and palynological micro-morphological characters were examined to explain their value in resolving the difficulty in identification. All species were amphistomatic but stomata on abaxial surface were more abundant. Taxonomically significant epidermal character including stomata type, trichomes (unicellular, multicellular, and capitate) and epidermal cells shapes (polygonal and irregular) were also observed. Pollens of this family are Polypantoporate, pores large, spheroidal, mesoporous region is sparsely to scabrate, densely psilate, and spinulose. All these characters can be active at species level for identification purpose. This study indicates that at different taxonomic levels, LM and SEM pollen and epidermal morphology is explanatory and significant to identify species and genera. © 2018 Wiley Periodicals, Inc.

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

PubMed

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

2016-07-01

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. Copyright © 2016 The Author(s). Published by Elsevier GmbH.. All rights reserved.

Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora)

PubMed Central

2016-01-01

The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. PMID:26893959

Taxonomic revision of Neotropical Murdannia Royle (Commelinaceae)

PubMed Central

Pellegrini, Marco Octávio de Oliveira; Faden, Robert B.; de Almeida, Rafael Felipe

2016-01-01

Abstract This study provides a taxonomic revision for the Neotropical species of the genus Murdannia. Six species are recognized as native, including a new species and a new combination, while two Asian species are recognized as invasive. We present an identification key, a table summarizing the morphologic differences among the species, a new synonym, six lectotypifications, a distribution map, and descriptions, comments and photographic plates for each species. We also provide comments on the morphology of the Neotropical species of Murdannia, comparing them with the Paleotropical species, and a discussion of inflorescence architecture in the genus as a whole. PMID:28127236

Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae)

PubMed Central

Fonseca, Luiz Henrique M.; Cabral, Simone Miranda; Agra, Maria de Fátima; Lohmann, Lúcia G.

2015-01-01

Abstract Dolichandra is a genus of lianas found in dry and wet Neotropical forests. The genus currently includes eight species and is well characterized by molecular and morphological synapomorphies. Here, Macfadyena hispida (DC.) Seemann is removed from synonomy with Dolichandra uncata (Andrews) L.G. Lohmann based on the presence of the hispid indument, vinaceus ovary, long fruits, and winged seeds. The combination Dolichandra hispida (DC.) L.H. Fonseca & L.G. Lohmann, comb. nov. is proposed, increasing the number of accepted species of Dolichandra to nine. A taxonomic key for all species of Dolichandra is presented. PMID:25878548

Taxonomic history and current status of Stachybotrys chartarum and related species.

PubMed

Li, D-W; Yang, C S

2005-01-01

The fungus Stachybotrys chartarum is the type species of the genus Stachybotrys. It is a cellulolytic saprophyte with a worldwide distribution and is frequently recovered in water-damaged buildings. Three isolates of S. chartarum were studied morphologically from single-spore isolations. Significant differences were found with the sizes, lengths, width, and L/W ratio of conidia and phialides among the isolates. QPCR analysis on S. chartarum, S. yunnanensis, S. chlorohalonata, S. elegans, S. microspora, and S. nephrospora showed that the primers and probe for detecting S. chartarum used by commercial laboratories were not able to differentiate S. chartarum from S. chlorohalonata and S. yunnanensis. Results suggested that S. chartarum may not be well delineated even after S. chlorohalonata was recently segregated from the species complex. Further study on the taxonomic status of the epithet S. chartarum is necessary. Six species of Stachybotrys are present indoors. Differentiation of Stachybotrys chartarum from S. chlorohalonata, and S. yunnanensis can be challenging using either morphological or QPCR methods. Caution should be taken to identify S. chartarum and closely related species and to explain their health effects implication for indoor air quality investigations.

Individual Differences in the Strength of Taxonomic versus Thematic Relations

ERIC Educational Resources Information Center

Mirman, Daniel; Graziano, Kristen M.

2012-01-01

Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) on the basis of shared features or thematically (eating breakfast, taking a dog for a walk, etc.) on the basis of participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a…

Taxonomic and ad hoc categorization within the two cerebral hemispheres.

PubMed

Shen, Yeshayahu; Aharoni, Bat-El; Mashal, Nira

2015-01-01

A typicality effect refers to categorization which is performed more quickly or more accurately for typical than for atypical members of a given category. Previous studies reported a typicality effect for category members presented in the left visual field/right hemisphere (RH), suggesting that the RH applies a similarity-based categorization strategy. However, findings regarding the typicality effect within the left hemisphere (LH) are less conclusive. The current study tested the pattern of typicality effects within each hemisphere for both taxonomic and ad hoc categories, using words presented to the left or right visual fields. Experiment 1 tested typical and atypical members of taxonomic categories as well as non-members, and Experiment 2 tested typical and atypical members of ad hoc categories as well as non-members. The results revealed a typicality effect in both hemispheres and in both types of categories. Furthermore, the RH categorized atypical stimuli more accurately than did the LH. Our findings suggest that both hemispheres rely on a similarity-based categorization strategy, but the coarse semantic coding of the RH seems to facilitate the categorization of atypical members.

Amazon plant diversity revealed by a taxonomically verified species list.

PubMed

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M; Bittrich, Volker; Celis, Marcela; Daly, Douglas C; Fiaschi, Pedro; Funk, Vicki A; Giacomin, Leandro L; Goldenberg, Renato; Heiden, Gustavo; Iganci, João; Kelloff, Carol L; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F P; Dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A; Nunes, Teonildes Sacramento; Pennington, Terry D; Pirani, José Rubens; Prance, Ghillean T; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Riina, Ricarda; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D; Taylor, Charlotte M; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E; Forzza, Rafaela Campostrini

2017-10-03

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

EFFECTS OF NONINDIGENOUS SPECIES ON THE TAXONOMIC DIVERSITY OF ESTUARINE ASSEMBLAGES

EPA Science Inventory

The effects of the few numerically dominant invasive species on benthic community abundance patterns has been documented in a number of estuaries. What is less appreciated is that the entire suite of nonindigenous species may alter the taxonomic composition of a community or biog...

Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru

PubMed Central

Aguilar, César; Wood Jr, Perry L.; Cusi, Juan C.; Guzmán, Alfredo; Huari, Frank; Lundberg, Mikael; Mortensen, Emma; Ramírez, César; Robles, Daniel; Suárez, Juana; Ticona, Andres; Vargas, Víctor J.; Venegas, Pablo J.; Sites Jr, Jack W.

2013-01-01

Abstract Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes) to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided. PMID:24453545

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

PubMed

Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

2017-01-04

The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A complex ligase ribozyme evolved in vitro from a group I ribozyme domain

NASA Technical Reports Server (NTRS)

Jaeger, L.; Wright, M. C.; Joyce, G. F.; Bada, J. L. (Principal Investigator)

1999-01-01

Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.

Selective transformations of complex molecules are enabled by aptameric protective groups

NASA Astrophysics Data System (ADS)

Bastian, Andreas A.; Marcozzi, Alessio; Herrmann, Andreas

2012-10-01

Emerging trends in drug discovery are prompting a renewed interest in natural products as a source of chemical diversity and lead structures. However, owing to the structural complexity of many natural compounds, the synthesis of derivatives is not easily realized. Here, we demonstrate a conceptually new approach using oligonucleotides as aptameric protective groups. These block several functionalities by non-covalent interactions in a complex molecule and enable the highly chemo- and regioselective derivatization (>99%) of natural antibiotics in a single synthetic step with excellent conversions of up to 83%. This technique reveals an important structure-activity relationship in neamine-based antibiotics and should help both to accelerate the discovery of new biologically active structures and to avoid potentially costly and cumbersome synthetic routes.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2016-11-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil

Using citizen science to bridge taxonomic discovery with education and outreach.

PubMed

von Konrat, Matt; Campbell, Thomas; Carter, Ben; Greif, Matthew; Bryson, Mike; Larraín, Juan; Trouille, Laura; Cohen, Steve; Gaus, Eve; Qazi, Ayesha; Ribbens, Eric; Livshultz, Tatyana; Walker, Taylor J; Suwa, Tomomi; Peterson, Taylor; Rodriguez, Yarency; Vaughn, Caitlin; Yang, Christina; Aburahmeh, Selma; Carstensen, Brian; de Lange, Peter; Delavoi, Charlie; Strauss, Kalman; Drag, Justyna; Aguero, Blanka; Snyder, Chris; Martinec, Joann; Smith, Arfon

2018-02-01

Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss. Efforts to fully leverage collections are impeded by a lack of trained taxonomists and a lack of interest and engagement by the public. We provide a model of a crowd-sourced data collection project that produces quality taxonomic data sets and empowers citizen scientists through real contributions to science. Entitled MicroPlants, the project is a collaboration between taxonomists, citizen science experts, and teachers and students from universities and K-12. We developed an online tool that allows citizen scientists to measure photographs of specimens of a hyper-diverse group of liverworts from a biodiversity hotspot. Using the MicroPlants online tool, citizen scientists are generating high-quality data, with preliminary analysis indicating non-expert data can be comparable to expert data. More than 11,000 users from both the website and kiosk versions have contributed to the data set, which is demonstrably aiding taxonomists working toward establishing conservation priorities within this group. MicroPlants provides opportunities for public participation in authentic science research. The project's educational component helps move youth toward engaging in scientific thinking and has been adopted by several universities into curriculum for both biology and non-biology majors.

Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities.

PubMed

Wang, Shi-Jun; Bateman, Richard M; Spencer, Alan R T; Wang, Jun; Shao, Longyi; Hilton, Jason

2017-01-01

Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian-Permian Epochs (323-252 Ma) but are of controversial taxonomic affinity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids, progymnosperms, or the extant eusporangiate fern Tmesipteris. Previously identified noeggerathialeans lacked anatomical preservation, limiting taxonomic comparisons to their external morphology and spore structure. We here document from the upper Permian of China the first anatomically preserved noeggerathialeans, which enhance the perceived distinctiveness of the group and better indicate its systematic affinity. We describe in detail the newly discovered, anatomically preserved heterosporous strobilus Dorsalistachya quadrisegmentorum, gen. et sp. nov., and redescribe its suspected foliar correlate, the pinnate leaf Plagiozamites oblongifolius. Plagiozamites possesses an omega (Ω)-shaped vascular trace and prominent cortical secretory cavities-a distinctive anatomical organization that is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggesting that they are homologs of leaf pinnae. If so, the "strobilus" is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchical level below true sporophylls. The "sporophylls" bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinal rows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as a single unit. Dorsalistachya presents a unique combination of reproductive features that amply justifies establishment of a new family, Dorsalistachyaceae. Noeggerathiales represent a distinct taxonomic Order of free-sporing plants that most resembles early-divergent eusporangiate ferns and the more derived among the

Different influences on lexical priming for integrative, thematic, and taxonomic relations

PubMed Central

Jones, Lara L.; Golonka, Sabrina

2012-01-01

Word pairs may be integrative (i.e., combination of two concepts into one meaningful entity; e.g., fruit—cake), thematically related (i.e., connected in time and place; e.g., party—cake), and/or taxonomically related (i.e., shared features and category co-members; e.g., muffin—cake). Using participant ratings and computational measures, we demonstrated distinct patterns across measures of similarity and co-occurrence, and familiarity for each relational construct in two different item sets. In a standard lexical decision task (LDT) with various delays between prime and target presentation (SOAs), target RTs and priming magnitudes were consistent across the three relations for both item sets. However, across the SOAs, there were distinct patterns among the three relations on some of the underlying measures influencing target word recognition (LSA, Google, and BEAGLE). These distinct patterns suggest different mechanisms of lexical priming and further demonstrate that integrative relations are distinct from thematic and taxonomic relations. PMID:22798950

The Impact of Communication Mode and Task Complexity on Small Group Performance and Member Satisfaction.

ERIC Educational Resources Information Center

Carey, Jane M.; Kacmar, Charles, J.

1997-01-01

It is often presumed that software technology will increase group productivity, but this may not be the case. Examines the impact of technology on time-to-complete-task, member satisfaction, perceived information load, number of contributing transactions, and task complexity. Three appendices provide examples of complex and simple tasks and the…

A taxonomic index, with names of descriptive authorities of termite genera and species: An accompaniment to Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, Editors. 2011. Springer, Dordrecht. 576 pp.)

PubMed Central

Bignell, D. E.; Jones, D. T.

2014-01-01

Abstract Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, (Editors), Springer, Dordrecht, 576pp, ISBN 978-90-481-3976-7, e-ISBN 978-90-481-3977-4, DOI 10.1007/978-90-481-3977-4) was published in 2011. With the agreement of the publishers, we give a taxonomic index of the book comprising 494 termite entries, 103 entries of other multicellular animal species mentioned as associates or predators of termites, with 9 fungal, 60 protist, and 64 prokaryote identities, which are listed as termite symbionts ( sensu stricto ). In addition, we add descriptive authorities for living (and some fossil) termite genera and species. Higher taxonomic groupings for termites are indicated by 25 code numbers. Microorganisms (prokaryotes, protists, and fungi) are listed separately, using broad modern taxonomic affiliations from the contemporary literature of bacteriology, protozoology, and mycology. PMID:25368037

Molecular studies on the species complex of Trichosirocalus horridus in the biological control of Carduinae weeds.

USDA-ARS?s Scientific Manuscript database

The genus Trichosirocalus Colonnelli, 1979, (Coleoptera, Curculionidae, Ceutorhynchinae) includes 17 Palaearctic species mainly feeding on Plantaginaceae and Asteraceae. We studied the taxonomic status of the species complex of Trichosirocalus horridus (TH) by means of molecular markers. We used bot...

When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice.

PubMed

Martynov, Alexander; Ishida, Yoshiaki; Irimura, Seiichi; Tajiri, Rie; O'Hara, Timothy; Fujita, Toshihiko

2015-01-01

Current taxonomy offers numerous approaches and methods for species delimitation and description. However, most of them are based on the adult characters and rarely suggest a dynamic representation of developmental transformations of taxonomically important features. Here we show how the underestimation of ontogenetic changes may result in long term lack of recognition of a new species of one of the most common ophiacanthid brittle stars (Echinodermata: Ophiuroidea) from the North Pacific. Based on vast material collected predominantly by various Japanese expeditions in the course of more than 50 years, and thorough study of appropriate type material, we revise the complex of three common species of the ophiuroid genus Ophiacantha which have been persistently confused with each other. The present study thus reveals the previously unrecognized new species Ophiacantha kokusai sp.nov. which is commonly distributed off the Pacific coast of Japan. The new species shows developmental differentiation from the closely related species Ophiacantha rhachophora H. L. Clark, 1911 and retains clearly expressed early juvenile features in the adult morphology. Another species, Ophiacantha clypeata Kyte, 1977, which had been separated from O. rhachophora, is in turn shown to be just a juvenile stage of another North Pacific species, Ophiacantha trachybactra H.L. Clark, 1911. For every species, detailed morphological data from both adult and juvenile specimens based on scanning electron microscopy are presented. A special grinding method showing complex internal features has been utilized for the first time. For all three species in this complex, a clear bathymetric differentiation is revealed: O. rhachophora predominantly inhabits shallow waters, 0-250 m, the new species O. kokusai lives deeper, at 250-600 m, and the third species, O. trachybactra, is found at 500-2,000 m. The present case clearly highlights the importance of considering developmental transformations, not only for

[Taxonomic and functional diversity of the bycatch fishes community of trawl fishing from Northern Gulf of California, Mexico].

PubMed

Herrera-Valdivia, Eloísa; López-Martínez, Juana; Castillo Vargasmachuca, Sergio; García-Juárez, Rosa

2016-06-01

The Northern Gulf of California (NGC) is a mega diverse area of high endemism with major economic interest because of the multi-specific fisheries developed, mainly shrimp. There is a lack of recent studies on bycatch fish assemblages, so during the fishing seasons from 2009-2010 and 2010-2011, on board 13 shrimp boats, 14 commercial fishing trips were performed from 5 m - 90 m in depth with a total of 119 catches. The 119 catches were analyzed to assess fish community structure using taxonomic diversity indices to detect changes in the community following the taxonomic distinctness average Δ+ and the diversity index Δ* (TAXDEST of the PRIMER v6 program). To confirm the structure of functional groups, we considered similarities of ecologic and morphologic traits among species. The results showed that the indices Δ+ and Δ* were within the expected average and confidence intervals at 95%, finding significant differences between the indices. The analyses showed a well-structured community because of the great variety of forms and functions of the species within the community. In the community of the functional groups, reproduction was the ecological attribute that contributed the most to their structure. The community structure was represented by intermediate trophic levels (3-3.9), preferably primary and secondary carnivores within the trophic categories of predators of benthic ichthyo-fauna that belong to demersal species of soft bottoms and mostly fusiform body. To conclude, the NGC showed high functional redundancy according to the estimated functional groups, thus the ecosystem was considered stable and with great diversity. This type of studies should be followed using fishing and environmental effort due to the great biological and ecologic importance in the area.

Identification of Rays through DNA Barcoding: An Application for Ecologists

PubMed Central

Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey J. A.; Austin, Chris M.

2012-01-01

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. PMID:22701556

Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

PubMed Central

Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

2013-01-01

A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Genome-Based Taxonomic Classification of Bacteroidetes

PubMed Central

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter; Göker, Markus

2016-01-01

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved. PMID:28066339

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

PubMed

Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

2018-04-18

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

PubMed

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

PubMed Central

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

Renormalization group approach to power-law modeling of complex metabolic networks.

PubMed

Hernández-Bermejo, Benito

2010-08-07

In the modeling of complex biological systems, and especially in the framework of the description of metabolic pathways, the use of power-law models (such as S-systems and GMA systems) often provides a remarkable accuracy over several orders of magnitude in concentrations, an unusually broad range not fully understood at present. In order to provide additional insight in this sense, this article is devoted to the renormalization group analysis of reactions in fractal or self-similar media. In particular, the renormalization group methodology is applied to the investigation of how rate-laws describing such reactions are transformed when the geometric scale is changed. The precise purpose of such analysis is to investigate whether or not power-law rate-laws present some remarkable features accounting for the successes of power-law modeling. As we shall see, according to the renormalization group point of view the answer is positive, as far as power-laws are the critical solutions of the renormalization group transformation, namely power-law rate-laws are the renormalization group invariant solutions. Moreover, it is shown that these results also imply invariance under the group of concentration scalings, thus accounting for the reported power-law model accuracy over several orders of magnitude in metabolite concentrations. Copyright 2010 Elsevier Ltd. All rights reserved.

Postembryonic development of hard jaws (trophi) in a species belonging to the Brachionus plicatilis complex (Rotifera, Monogononta): a morphometric analysis.

PubMed

Fontaneto, Diego; Melone, Giulio

2006-04-01

The presence of hard jaws (trophi), with species-specific shape and size, is a taxonomic feature of Rotifera, a group of microscopic metazoans. Since trophi are used to discriminate among species, it is important to know whether these structures change in taxonomically important ways during postembryonic development. Using both SEM and optical images, we analyzed more than 100 individuals of a single clonal lineage of a monogonont rotifer, Brachionus plicatilis, in order to describe body and trophi development after hatching. Body size, expressed as lorica width and length, was isometrically related to age of the animals only during preadult stages. Trophi size, expressed as length of the different parts, was unrelated to either age or body size. Therefore, trophi elements do not grow after hatching in B. plicatilis. Despite the dimensional invariance with age, some differences in trophi size among individuals of the same clone were recorded. No difference in left-right asymmetry of the trophi was shown; the asymmetric elements of the trophi named rami consistently had the right ramus longer than the left. This constancy is in contrast to the reported trophi asymmetries in bdelloid rotifers, in which left-right asymmetries are not constant within clonal lineages. In conclusion, we suggest that also trophi size, constant within the analyzed clone, may be used as an additional taxonomic feature to help in the discrimination of taxa within the B. plicatilis complex of cryptic species. Copyright (c) 2006 Wiley-Liss, Inc.

Group living in squamate reptiles: a review of evidence for stable aggregations.

PubMed

Gardner, Michael G; Pearson, Sarah K; Johnston, Gregory R; Schwarz, Michael P

2016-11-01

How sociality evolves and is maintained remains a key question in evolutionary biology. Most studies to date have focused on insects, birds, and mammals but data from a wider range of taxonomic groups are essential to identify general patterns and processes. The extent of social behaviour among squamate reptiles is under-appreciated, yet they are a promising group for further studies. Living in aggregations is posited as an important step in the evolution of more complex sociality. We review data on aggregations among squamates and find evidence for some form of aggregations in 94 species across 22 families. Of these, 18 species across 7 families exhibited 'stable' aggregations that entail overlapping home ranges and stable membership in long-term (years) or seasonal aggregations. Phylogenetic analysis suggests that stable aggregations have evolved multiple times in squamates. We: (i) identify significant gaps in our understanding; (ii) outline key traits which should be the focus of future research; and (iii) outline the potential for utilising reproductive skew theory to provide insights into squamate sociality. © 2015 Cambridge Philosophical Society.

Amazon plant diversity revealed by a taxonomically verified species list

PubMed Central

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M.; Bittrich, Volker; Celis, Marcela; Daly, Douglas C.; Fiaschi, Pedro; Funk, Vicki A.; Giacomin, Leandro L.; Heiden, Gustavo; Iganci, João; Kelloff, Carol L.; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F. P.; dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A.; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A.; Nunes, Teonildes Sacramento; Pennington, Terry D.; Pirani, José Rubens; Prance, Ghillean T.; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D.; Taylor, Charlotte M.; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E.; Forzza, Rafaela Campostrini

2017-01-01

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests. PMID:28923966

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping.

PubMed

Mukherjee, Sumanta; Warwicker, Jim; Chandra, Nagasuma

2015-07-01

T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.

Origin of the flax cultivar 'Appar' and its position within the Linum perenne complex

Treesearch

Rosemary L. Pendleton; Stanley G. Kitchen; Joann Mudge; E. Durant McArthur

2008-01-01

The 'Appar' flax germplasm was originally released by the USDA Soil Conservation Service as a cultivar of Linum lewisii. The observation that 'Appar' is heterostylic, a key taxonomic character distinguishing Lewis flax from other members of the Linum perenne complex, created a need for further study in order to...

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

PubMed

Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

Insights into discriminating environmental quality status using taxonomic distinctness based on a small species pool of ciliated protozoa in marine ecosystems.

PubMed

Jiang, Yong; Xu, Henglong; Warren, Alan

2014-01-15

The objective of this study was to determine the feasibility of developing a protocol for assessing marine water quality based on taxonomic relatedness within a small pool of planktonic ciliates. An annual dataset was compiled based on samples collected biweekly at five sites, with a gradient of environmental stress, during a 1-year cycle in Jiaozhou Bay, northern China. A total of 60 species, belonging to 17 genera 10 families, 5 orders and 2 classes of the phylum Ciliophora, were identified. Among five orders, Tintinnida showed a low variability mainly at species level whereas the other orders (especially Strombidiida and Choreotrichida, although with the exception of the genus Strombidium) represented a high variability at higher taxonomic ranks (e.g. family or order). Mantel analyses showed that spatial patterns of the ciliate assemblages, with tinitinnids and Strombidium spp. excluded, were significantly correlated with those of the total planktonic ciliate communities in terms of their response to environmental status. The average taxonomic distinctness (Δ(+)) based on the small species pool was significantly negatively correlated with the changes in concentrations of nutrients (P<0.05). Furthermore, the paired indices of Δ(+) and the variation in taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that it is possible to assess the status of marine water quality using the taxonomic relatedness within a small pool of planktonic ciliates. © 2013.

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

Brief communication: a cranial morphometric assessment of the taxonomic affinities of Trachypithecus auratus (E. Geoffroy, 1812 primates: Colobinae) with a reassessment of the T. auratus type specimen.

PubMed

Ingicco, Thomas; Balzeau, Antoine; Callou, Cécile; Fitriana, Yuliana Sulistya

2011-10-01

The debate over the taxonomic position and affinities of Trachypithecus auratus has been ongoing since its identification by E. Geoffroy Saint-Hilaire in 1812. The type specimen of this species is housed in Muséum national d'Histoire naturelle in Paris (MNHN-ZM 2005-912). This point is debated due to the complex and fluctuating taxonomy of Southeast Asian Colobinae (Brandon-Jones et al.: Int J Primatol 25 (2004) 97-164) and to the fact that this individual is represented by a mounted skeleton. By means of 3D medical imaging methodologies we describe for the first time the cranial anatomy of the specimen MNHN-ZM 2005-912 and compare it with other Trachypithecus species, in order to test the molecular systematic hypotheses for affinities among the T. auratus-T. cristatus group. We ascertain the taxonomic attribution of this individual to the species Trachypithecus auratus species. The most diagnostic characters shared by the type specimen and Trachypithecus auratus compared to other species of Trachypithecus are the rounded orbits and the straight facial profile. We then try to clarify the inconsistencies concerning the geographical provenance of the type. The island of Java appears to be the most probable locality from a cluster analysis based on linear morphometry. After this approach and a discriminant analysis, a northeastern Javanese provenance of this specimen, as proposed by Brandon-Jones et al. (Int J Primatol 25 (2004) 97-164) is dubious. Finally we provide 3D models of the skull and the endocast, and a list of cranial landmark coordinates of the holotype for future research. Copyright © 2011 Wiley-Liss, Inc.

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

PubMed

Alsop, Eric B; Raymond, Jason

2013-01-01

Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

PubMed

Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

2014-04-01

The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. © 2013 Society for Conservation Biology.

Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

PubMed Central

Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

2012-01-01

Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

The coordination chemistry of group 15 element ligand complexes--a developing area.

PubMed

Scheer, Manfred

2008-09-07

A survey of the contemporary challenges of the field of unsubstituted group 15 element ligand complexes (excluding N) is given. The focus of the article is on the coordination chemistry behaviour of such E(n) ligand complexes. This field is subdivided into two areas of reactivity: E(n) ligand complexes with (i) noncoordinated Lewis-acidic cations and (ii) Lewis-acidic coordination compounds containing at least one permanently coordinating ligand. In the latter case, insoluble 1D and 2D polymers respectively are obtained; however, under special conditions soluble, spherical, fullerene-like giant molecules are formed. These nano-sized molecules are up to 2.4 nm in diameter and are able to encapsulate small molecules in their holes. In contrast, the first-mentioned field uses weakly coordinating anions to obtain readily soluble di- and polycationic products. These show depolymerisation tendencies in solution under the formation of oligomer-monomer equilibria and thus reveal dynamic supramolecular aggregation processes.

Notes on the taxonomic position of several species of the genus Diphascon (Tardigrada, Hypsibiidae).

PubMed

Tumanov, Denis V

2018-03-20

For this paper I analysed the descriptions of all species, attributed to the genus Diphascon Plate, 1889, to ascertain if they fit the diagnosis of this genus, provided by Bertolani et al. 2014. Thirty four species (the majority of the species diversity classified within the genus) fully match its emended diagnosis, while three: Diphascon opisthoglyptum Maucci, 1987, Diphascon procerum Pilato, Sabella Lisi, 2014 and Diphascon ziliense Lisi, Sabella Pilato, 2014, demonstrate a combination of characters, typical to the genus Pilatobius Bertolani et al., 2014. I propose the transfer these three species to the genus Pilatobius, thus their new taxonomic positions are as follows: Pilatobius opisthoglyptus (Maucci, 1987) comb. nov., Pilatobius procerus (Pilato, Sabella Lisi, 2014) comb. nov. and Pilatobius ziliense (Lisi, Sabella Pilato, 2014) comb. nov. Descriptions of three other Diphascon species (Diphascon mariae (Mihelčič, 1951), Diphascon rivulare (Mihelčič, 1967) and Diphascon punctatum (Iharos, 1962)) contain too little detail to conclude on their taxonomic position. The species Pilatobius halapiense (Iharos, 1964) was erroneously transferred from the genus Diphascon, and here I suggest it is transferred back to Diphascon. The new taxonomic position of this species is: Diphascon halapiense (Iharos, 1964) comb. nov. Emended list of species, attributed to the genus Diphascon is given.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

PubMed

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-08-11

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

PubMed Central

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A.; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J.; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A.; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H.; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J.; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E.; Hendrix, Stephen D.; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M. E.; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A.; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S.; Morales, Carolina L.; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G.; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A.; Persson, Anna S.; Petanidou, Theodora; Poveda, Katja; Power, Eileen F.; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H.; Roulston, T’ai; Rousseau, Laurent; Sadler, Jonathan P.; Samnegård, Ulrika; Schellhorn, Nancy A.; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H.; Steffan-Dewenter, Ingolf; Stout, Jane C.; Tonietto, Rebecca K.; Tscharntke, Teja; Tylianakis, Jason M.; Verboven, Hans A. F.; Vergara, Carlos H.; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-01-01

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

Characterization of the Sukinda and Nausahi ultramafic complexes, Orissa, India by platinum-group element geochemistry

USGS Publications Warehouse

Page, N.J.; Banerji, P.K.; Haffty, J.

1985-01-01

Samples of 20 chromitite, 14 ultramafic and mafic rock, and 9 laterite and soil samples from the Precambrian Sukinda and Nausahi ultramafic complexes, Orissa, India were analyzed for platinum-group elements (PGE). The maximum concentrations are: palladium, 13 parts per billion (ppb); platinum, 120 ppb; rhodium, 21 ppb; iridium, 210 ppb; and ruthenium, 630 ppb. Comparison of chondrite-normalized ratios of PGE for the chromitite samples of lower Proterozoic to Archean age with similar data from Paleozoic and Mesozoic ophiolite complexes strongly implies that these complexes represent Precambrian analogs of ophiolite complexes. This finding is consistent with the geology and petrology of the Indian complexes and suggests that plate-tectonic and ocean basin developement models probably apply to some parts of Precambrian shield areas. ?? 1985.

Flexible taxonomic assignment of ambiguous sequencing reads

PubMed Central

2011-01-01

Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results. PMID:21211059

Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)

PubMed Central

Drotz, Marcus K.; Brodin, Tomas; Nilsson, Anders N.

2015-01-01

Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation. PMID:26619278

Knowledge-based grouping of modeled HLA peptide complexes.

PubMed

Kangueane, P; Sakharkar, M K; Lim, K S; Hao, H; Lin, K; Chee, R E; Kolatkar, P R

2000-05-01

Human leukocyte antigens are the most polymorphic of human genes and multiple sequence alignment shows that such polymorphisms are clustered in the functional peptide binding domains. Because of such polymorphism among the peptide binding residues, the prediction of peptides that bind to specific HLA molecules is very difficult. In recent years two different types of computer based prediction methods have been developed and both the methods have their own advantages and disadvantages. The nonavailability of allele specific binding data restricts the use of knowledge-based prediction methods for a wide range of HLA alleles. Alternatively, the modeling scheme appears to be a promising predictive tool for the selection of peptides that bind to specific HLA molecules. The scoring of the modeled HLA-peptide complexes is a major concern. The use of knowledge based rules (van der Waals clashes and solvent exposed hydrophobic residues) to distinguish binders from nonbinders is applied in the present study. The rules based on (1) number of observed atomic clashes between the modeled peptide and the HLA structure, and (2) number of solvent exposed hydrophobic residues on the modeled peptide effectively discriminate experimentally known binders from poor/nonbinders. Solved crystal complexes show no vdW Clash (vdWC) in 95% cases and no solvent exposed hydrophobic peptide residues (SEHPR) were seen in 86% cases. In our attempt to compare experimental binding data with the predicted scores by this scoring scheme, 77% of the peptides are correctly grouped as good binders with a sensitivity of 71%.

Application of the Red-List Index at a national level for multiple species groups.

PubMed

Juslén, Aino; Hyvärinen, Esko; Virtanen, Laura K

2013-04-01

The International Union for Conservation of Nature (IUCN) Red List Index (RLI) is recognized as one of the key indicators of trends in the status of species. The red-list assessment done by Finnish authorities of species in Finland is taxonomically one of the most extensive national assessments. We used the Finnish Red Lists from 2000 and 2010 to calculate for the first time the national RLIs for 11 taxonomic groups at different trophic levels and with different life cycles. The red-list index is calculated on the basis of changes in red-list categories and indicates trends in the status of biological diversity of sets of species. The RLI value ranges from 0 to 1. The lower the value the faster the set of species is heading toward extinction. If the value is 1, all species in the set are least concern and if the value is 0, all species are (regionally) extinct. The overall RLI of Finnish species decreased. This means that, in Finland, these taxonomic groups were heading toward extinction faster in 2010 than in 2000. Of the analyzed groups of organisms, RLIs of 5 decreased and RLIs of 6 increased. At the national level, the RLIs and status trends varied markedly between species groups. Thus, we concluded that generalizations on the basis of RLIs of a few taxa only may yield a biased view of ongoing trends in the status of biological diversity at the species level. In addition, one overall RLI that includes many different species groups may also be misleading if variation in RLI among species groups is not considered and if RLI values are not presented separately for each group. © 2013 Society for Conservation Biology.

Taxonomic changes and description of two new species for the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico.

PubMed

RamÍrez-Reyes, Tonatiuh; Flores-Villela, Oscar

2018-04-10

An integrative taxonomy approach was implemented based on analysis of genetic, phylogenetic, morphological and ecological data to identify the cryptic diversity within the Phyllodactylus lanei complex. At least six species can be identified, of which four are currently considered subspecies: Phyllodactylus lanei, Phyllodactylus rupinus, Phyllodactylus isabelae, Phyllodactylus lupitae and two corresponding to undescribed taxa, which are identified and described in this contribution. These differ from other Mexican geckos in several characters: genetic distance (DNAmt), position in molecular phylogeny (concatened data DNAmt+DNAnu), species tree, morphological characters such as snout-vent length, longitudinal scales, tubercles from head to tail, interorbital scales, scales across venter, third labial-snout scales and rows of tubercles across dorsum; there are also differences in their bioclimatic profiles (temperature and precipitation) and geographical distribution. The most recent studies on taxonomy and evolution of Mexican geckos (Phyllodactylus) show that the diversity of this group of reptiles is currently underestimated, suggesting that more research and conservation efforts are should be addressed at these lizards.

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

PubMed Central

Benítez-Benítez, Carmen; Fernández-Mazuecos, Mario; Martín-Bravo, Santiago

2017-01-01

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5’trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution. PMID:29281689

The Development of Second Language Writing Complexity in Groups and Individuals: A Longitudinal Learner Corpus Study

ERIC Educational Resources Information Center

Vyatkina, Nina

2012-01-01

This study explores the development of multiple dimensions of linguistic complexity in the writing of beginning learners of German both as a group and as individuals. The data come from an annotated, longitudinal learner corpus. The development of lexicogrammatical complexity is explored at 2 intersections: (a) between cross-sectional trendlines…

Novel type of red-shifted chlorophyll a antenna complex from Chromera velia: II. Biochemistry and spectroscopy.

PubMed

Bína, David; Gardian, Zdenko; Herbstová, Miroslava; Kotabová, Eva; Koník, Peter; Litvín, Radek; Prášil, Ondřej; Tichý, Josef; Vácha, František

2014-06-01

A novel chlorophyll a containing pigment-protein complex expressed by cells of Chromera velia adapted to growth under red/far-red illumination [1]. Purification of the complex was achieved by means of anion-exchange chromatography and gel-filtration. The antenna is shown to be an aggregate of ~20kDa proteins of the light-harvesting complex (LHC) family, unstable in the isolated form. The complex possesses an absorption maximum at 705nm at room temperature in addition to the main chlorophyll a maximum at 677nm producing the major emission band at 714nm at room temperature. The far-red absorption is shown to be the property of the isolated aggregate in the intact form and lost upon dissociation. The purified complex was further characterized by circular dichroism spectroscopy and fluorescence spectroscopy. This work thus identified the third different class of antenna complex in C. velia after the recently described FCP-like and LHCr-like antennas. Possible candidates for red antennas are identified in other taxonomic groups, such as eustigmatophytes and the relevance of the present results to other known examples of red-shifted antenna from other organisms is discussed. This work appears to be the first successful isolation of a chlorophyll a-based far-red antenna complex absorbing above 700nm unrelated to LHCI. Copyright © 2014 Elsevier B.V. All rights reserved.

Genome-Based Taxonomic Classification of Bacteroidetes

DOE PAGES

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; ...

2016-12-20

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Genome-Based Taxonomic Classification of Bacteroidetes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Separation of compounds with multiple -OH groups from dilute aqueous solutions via complexation with organoboronate. [1,2-propanediol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chow, Tina Kuo Fung.

1992-05-01

The complexing extractant agent investigated in this work is 3-nitrophenylboronic acid (NPBA) in its anionic form (NPB). NPBA and Aliquat 336 (quaternary amine) is dissolved in 2-ethyl-l-hexanol, and the extractant is contacted with aq. NaOH. Solutes investigated were 1,2-propanediol, glycerol, fructose, sorbitol and lactic acid. Batch extraction experiments were performed at 25{degree}C. Partition coefficients, distribution ratios and loadings are reported for varying concentrations of solute and NPB. All solutes complexed with NPB{sup {minus}}, with all complexes containing only one NPB{sup {minus}} per complex. The 1:1 complexation constants for the solutes glycerol, fructose and sorbitol follow trends similar to complexation withmore » B(OH){sub 4}{sup {minus}} (aq.), i.e. the complexation constants increase with increasing number of {minus}OH groups available for complexation. Assumption of 1:1 complex is not valid for 1, 2-propanediol, which showed overloading (more than one mole of solute complexed to one mole NPB{sup {minus}}) at higher concentrations. The {minus}OH group on the NPB{sup {minus}} which is left uncomplexed after one solute molecule had bound to the other two {minus}OH groups may be responsible for the overloading. Overloading is also observed in extraction of tactic acid, but through a different mechanism. It was found that TOMA{sup +} can extract lactic acid to an extent comparable to the uptake of lactic acid by NPB{sup {minus}}. The complexation is probably through formation of an acid-base ion pair. Losses of NPBA into the aqueous phase could lead to problems, poor economics in industrial separation processes. One way of overcoming this problem would be to incorporate the NPBA onto a solid support.« less

A taxonomic revision of the Neoserica (sensu lato) calva group (Coleoptera, Scarabaeidae, Sericini)

PubMed Central

Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke; Ahrens, Dirk

2014-01-01

Abstract The species of the Neoserica (sensu lato) calva group are revised. Neoserica calva Frey, 1972, comb. n. is redescribed. Thirteen new species are described from China and South Korea: Neoserica ailaoshanica sp. n., Neoserica anonyma sp. n., Neoserica calvoides sp. n., Neoserica gulinqingensis sp. n., Neoserica koelkebecki sp. n., Neoserica liangi sp. n., Neoserica luxiensis sp. n., Neoserica menghaiensis sp. n., Neoserica mengi sp. n., Neoserica taipingensis sp. n., Neoserica zheijangensis sp. n., Neoserica zhibenshanica sp. n., and Neoserica zongyuani sp. n. A key to Sericini genera with multilamellate antenna and species groups of Neoserica of mainland Asia as well as a key to species of the Neoserica calva group are provided. A map of species distribution is given, habitus and male genitalia are illustrated. PMID:25408610

Grouping methods for estimating the prevalences of rare traits from complex survey data that preserve confidentiality of respondents.

PubMed

Hyun, Noorie; Gastwirth, Joseph L; Graubard, Barry I

2018-03-26

Originally, 2-stage group testing was developed for efficiently screening individuals for a disease. In response to the HIV/AIDS epidemic, 1-stage group testing was adopted for estimating prevalences of a single or multiple traits from testing groups of size q, so individuals were not tested. This paper extends the methodology of 1-stage group testing to surveys with sample weighted complex multistage-cluster designs. Sample weighted-generalized estimating equations are used to estimate the prevalences of categorical traits while accounting for the error rates inherent in the tests. Two difficulties arise when using group testing in complex samples: (1) How does one weight the results of the test on each group as the sample weights will differ among observations in the same group. Furthermore, if the sample weights are related to positivity of the diagnostic test, then group-level weighting is needed to reduce bias in the prevalence estimation; (2) How does one form groups that will allow accurate estimation of the standard errors of prevalence estimates under multistage-cluster sampling allowing for intracluster correlation of the test results. We study 5 different grouping methods to address the weighting and cluster sampling aspects of complex designed samples. Finite sample properties of the estimators of prevalences, variances, and confidence interval coverage for these grouping methods are studied using simulations. National Health and Nutrition Examination Survey data are used to illustrate the methods. Copyright © 2018 John Wiley & Sons, Ltd.

A taxonomic index, with names of descriptive authorities of termite genera and species: an accompaniment to Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, Editors. 2011. Springer, Dordrecht. 576 pp.).

PubMed

Bignell, D E; Jones, D T

2014-01-01

Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, (Editors), Springer, Dordrecht, 576pp, ISBN 978-90-481-3976-7, e-ISBN 978-90-481-3977-4, DOI 10.1007/978-90-481-3977-4) was published in 2011. With the agreement of the publishers, we give a taxonomic index of the book comprising 494 termite entries, 103 entries of other multicellular animal species mentioned as associates or predators of termites, with 9 fungal, 60 protist, and 64 prokaryote identities, which are listed as termite symbionts (sensu stricto). In addition, we add descriptive authorities for living (and some fossil) termite genera and species. Higher taxonomic groupings for termites are indicated by 25 code numbers. Microorganisms (prokaryotes, protists, and fungi) are listed separately, using broad modern taxonomic affiliations from the contemporary literature of bacteriology, protozoology, and mycology. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

The use of bile - esculin agar for the taxonomic classification of the family Enterobacteriaceae.

PubMed

Edberg, S C; Pittman, S; Singer, J M

1977-01-01

Bile-esculin medium has been used for many years for the presumptive identification of group D Streptococcus. The test is based on the ability of a bacterium to grow in the presence of 40% bile and produce esculinase. 2935 strains of Enterobacteriaceae were inoculated onto bile-esculin agar slants and incubated at 35 C. Esculin hydrolysis was determined after 24 and 48 hours. At 24 hours of incubation esculin hydrolysis was limited to the genera Klebsiella, Enterobacter, Serratia, and the species P. vulgaris, P. rettgeri, and C. diversus. Not all strains of these species were positive, however. All other members of the family were negative. At 48 hours of incubation 37% of E. coli gave a positive reaction; all other Enterobacteriaceae which were negative at 24 hours remained negative. Esculin hydrolysis is a valuable test for the taxonomic classification of the family Enterobacteriaceae.

Zooplankton taxonomic and size diversity in Mediterranean coastal lagoons (NE Iberian Peninsula): Influence of hydrology, nutrient composition, food resource availability and predation

NASA Astrophysics Data System (ADS)

Badosa, Anna; Boix, Dani; Brucet, Sandra; López-Flores, Rocío; Gascón, Stéphanie; Quintana, Xavier D.

2007-01-01

The influence of hydrology, nutrient composition, food resource availability and predation on zooplankton taxonomic and size diversity was analyzed in several shallow lagoons of a Mediterranean salt marsh (Baix Ter Wetlands, NE Iberian Peninsula). Taxonomic diversity correlated better with variables related to the trophic state, such as nutrient concentrations, whereas size diversity was more sensitive to fish predation. However, the fish predation influence on the size diversity was only significant when fishes reached high densities. Under low fish densities no predation effects were observed and the food resource availability (FR a) appeared to be more important in structuring the zooplankton community. Nevertheless, the two diversity indexes showed opposite responses to this factor. With increasing FR a the taxonomic diversity increased and the size diversity decreased. Neither taxonomic nor size diversity of the zooplankton community correlated with other physical or biotic factors such as hydrological variability or macroinvertebrate predation. The relationships found suggest that the size diversity is mainly related to biotic interactions, such as fish predation or inter/intraspecific competition, while the taxonomic diversity appears to be more sensitive to abiotic factors such as the nutrient composition.

Deaf and hard of hearing adolescents' processing of pictures and written words for taxonomic categories in a priming task of semantic categorization.

PubMed

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written words for those of superordinate level (category names), in a priming task of semantic categorization. Stimulus onset asynchrony (SOA) was manipulated. The adolescents were less aware of taxonomic relations and were more likely to show the advantage of pictures over written words than their hearing counterparts. Their processing of exemplar primes steadily deepened as SOA increased, reaching its deepest level when SOA was 237 ms. Their processing of category names seemed immune to changes in SOA, probably because of their fuzzy representations of taxonomic categories of superordinate level.

COMPARISON OF TAXONOMIC, COLONY MORPHOTYPE AND PCR-RFLP METHODS TO CHARACTERIZE MICROFUNGAL DIVERSITY

EPA Science Inventory

We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological ...

Evaluation of the taxonomic status of populations assigned to Phyllomedusa hypochondrialis (Anura, Hylidae, Phyllomedusinae) based on molecular, chromosomal, and morphological approach

PubMed Central

2013-01-01

Background The taxonomic and phylogenetic relationships of the genus Phyllomedusa have been amply discussed. The marked morphological similarities among some species hamper the reliable identification of specimens and may often lead to their incorrect taxonomic classification on the sole basis of morphological traits. Phenotypic variation was observed among populations assigned to either P. azurea or P. hypochondrialis. In order to evaluate whether the variation observed in populations assigned to P. hypochondrialis is related to that in genotypes, a cytogenetic analysis was combined with phylogenetic inferences based on mitochondrial and nuclear sequences. Results The inter- and intra-population variation in the external morphology observed among the specimens analyzed in the present study do not reflect the phylogenetic relationships among populations. A monophyletic clade was recovered, grouping all the specimens identified as P. hypochondrialis and specimens assigned P. azurea from Minas Gerais state. This clade is characterized by conserved chromosomal morphology and a common C-banding pattern. Extensive variation in the nucleolar organizing region (NOR) was observed among populations, with four distinct NOR positions being recognized in the karyotypes. Intra-population polymorphism of the additional rDNA clusters observed in specimens from Barreiras, Bahia state, also highlights the marked genomic instability of the rDNA in the genome of this group. Based on the topology obtained in the phylogenetic analyses, the re-evaluation of the taxonomic status of the specimens from the southernmost population known in Brazil is recommended. Conclusions The results of this study support the need for a thorough revision of the phenotypic features used to discriminate P. azurea and P. hypochondrialis. The phylogenetic data presented here also contribute to an extension of the geographic range of P. hypochondrialis, which is known to occur in the Amazon basin and

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

PubMed

Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

2016-03-16

The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.

PubMed

Almeida, Alexandre; Mitchell, Alex L; Tarkowska, Aleksandra; Finn, Robert D

2018-05-01

Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene. We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently <2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline. Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision, and/or computational performance required.

How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

PubMed

Munoz, François; Ramesh, B R; Couteron, Pierre

2014-08-01

Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

Documenting taxonomic data quality for field fish identifications: a proposal for national surveys

EPA Science Inventory

The U.S. Environmental Protection Agency is in the midst of a multiyear series of natinal surveys of water resource conditions. Because communicating ecological condition is the primary objective of the surveys, quantitative biological indicators are key. Thus, if raw taxonomic d...

A taxonomic revision of the Neoserica (sensu lato) pilosula group (Coleoptera, Scarabaeidae, Sericini)

PubMed Central

Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke; Ahrens, Dirk

2014-01-01

Abstract Nine new species of the Neoserica (sensu lato) pilosula Moser, 1915, group are described from China: Neoserica curvipenis sp. n., N. emeishanensis sp. n., N. lincangensis sp. n., N. ludingensis sp. n., N. lushuiana sp. n., N. rangshuiensis sp. n., N. shennongjiaensis sp. n., N. tianeana sp. n., and N. weibaoshanica sp. n. The lectotype of Neoserica pilosula Moser, 1915, is designated. Habitus and male genitalia are illustrated, a key to the species of the group and a map of species distribution are given. PMID:25317063

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

PubMed Central

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-01-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

NASA Astrophysics Data System (ADS)

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-10-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

PubMed Central

Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

2011-01-01

Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

PubMed

Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

2016-01-01

Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

Contribution of different functional groups to the diet of major predatory fishes at a seagrass meadow in northeastern Japan

NASA Astrophysics Data System (ADS)

Yamada, Katsumasa; Hori, Masakazu; Tanaka, Yoshiyuki; Hasegawa, Natsuki; Nakaoka, Masahiro

2010-01-01

We examined the variation in habitat use and diet of three dominant fish species ( Myoxocephalus brandti, Pholidapus dybowskii, and Pholis crassispina) in a seagrass meadow in the Akkeshi-ko estuary in northeastern Japan, where broad and dense Zostera marina beds exist, using a semi-quantitative census of the fishes and analyses of their stomach contents. Differences among the three fish species in the temporal variation in abundance of each age class (mainly 1- and 2-year age classes) indicated that the temporal pattern of utilization of the seagrass meadow were different among them. In the semi-quantitative dietary analysis, two prey categories, i.e., taxonomic group (order and suborder) and functional group, were used to explain the variation in prey composition with size-dependent changes. The six prey functional groups were classified based on the ecological traits of the prey, i.e., trophic level, size, and life type (habitat and behavior). Ontogenetic shifts in prey of the three fish species could be fully explained by a combination of the two prey categories, and not by the use of only one category (taxonomic or functional group). The pattern of ontogenetic shifts in prey differed among the fish species and size (age) classes. These results indicate that segregation of habitat (seagrass meadow) and prey group (taxonomic and functional group) is performed among the three species, which may contribute to their coexistence in this estuary.

Becoming a Bricoleur: Constructing Sculptures to Explore Complex and Troublesome Dimensions in Educational Research

ERIC Educational Resources Information Center

Selkrig, Mark Andrew

2014-01-01

During a recent research project, it became apparent that the conventional taxonomic, textual and linguistic devices used to develop the narrative of a manuscript would not allow me to make sense, or tell the complex story, of my inquiry. I needed to employ multimodal approaches to grapple with the project related to artists who work in…

Chironomus group classification according to the mapping of polytene chromosomes

NASA Astrophysics Data System (ADS)

Salleh, Syafinaz; Kutty, Ahmad Abas

2013-11-01

Chironomus is one of the important genera in Chironomidae family since they are widely diverse and abundance in aquatic ecosystem. Since Chironomus is very diverse, taxonomic work on this genus is very difficult and incomplete. Objective of this study is to form group classification of Chironomus according to the polytene chromosome mapping. The specific characteristics of polytene chromosomes in the salivary gland appeared to be particularly promising for taxonomic diagnosis of chironomid species. Chironomid larvae were collected from pristine sites at Sg. Langat and cultured in laboratory to reach fourth instar stage. The salivary glands were removed from larvae and chromosomes were stained with aceto orcein. Results showed that polytene chromosomes of Chironomus comprise of three long metacentric or submetacentric arms (BF, CD and AE arms) and one short acrocentric (G arm). In regards to nucleolar organizing region (NOR), Balbiani ring (BR), puffings and chromosome rearrangement, a number of four groups of different banding patterns were found. Two groups called as G group A and B have common NOR on arm BF and BR on arm G. However, group A has rearrangement pattern on arm CD and not in group B. This makes group B separated from group A. Another two groups called as groups C and D do not have common NOR on arm BF and also BR on arm G. Groups C and D were separated using arms G and arm AE. At arm G, only group C rearrangement pattern at unit 23c whereas group D was found to have large NOR at arm G and as well as arm AE, only group D has rearrangement pattern at unit 12c. This study indicates that chromosome arrangement could aid in revealing Chironomus diversity.

Complexes of monocationic Group 13 elements with pentaphospha- and pentaarsaferrocene.

PubMed

Fleischmann, Martin; Welsch, Stefan; Krauss, Hannes; Schmidt, Monika; Bodensteiner, Michael; Peresypkina, Eugenia V; Sierka, Marek; Gröger, Christian; Scheer, Manfred

2014-03-24

Reactions of the sandwich complexes [Cp*Fe(η(5)-E5)] (Cp*=η(5)-C5Me5; E=P (1), As (2)) with the monovalent Group 13 metals Tl(+), In(+), and Ga(+) containing the weakly coordinating anion [TEF] ([TEF]=[Al{OC(CF3)3}4](-)) are described. Here, the one-dimensional coordination polymers [M(μ,η(5):η(1 -E5 FeCp*)3]n [TEF]n (E=P, M=Tl (3 a), In (3 b), Ga (3 c); E=As, M=Tl (4 a), In (4 b)) are obtained as sole products in good yields. All products were analyzed by single-crystal X-ray diffraction, revealing a similar assembly of the products with η(5)-bound E5 ligands and very weak σ-interactions between one P or As atom of the ring to the neighbored Group 13 metal cation. By exchanging the [TEF] anion of 4 a for the larger [FAl] anion ([FAl]=[FAl{OC6F10(C6F5)}3](-)), the coordination compound [Tl{(η(5)-As5)FeCp*}3][FAl] (5) without any σ-interactions of the As5-ring is obtained. All products are readily soluble in CH2 Cl2 and exhibit a dynamic coordination behavior in solution, which is supported by NMR spectroscopy and ESI-MS spectrometry as well as by osmometric molecular-weight determination. For a better understanding of the proceeding equilibrium DFT calculations of the cationic complexes were performed for the gas phase and in solution. Furthermore, the (31)P{(1)H} magic-angle spinning (MAS) NMR spectra of 3 a-c are presented and the first crystal structure of the starting material 2 was determined. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Taxonomic and Numerical Resolutions of Nepomorpha (Insecta: Heteroptera) in Cerrado Streams

PubMed Central

Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

2014-01-01

Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

Taxonomic and numerical resolutions of nepomorpha (insecta: heteroptera) in cerrado streams.

PubMed

Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

2014-01-01

Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

PubMed

Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

2015-11-01

The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

PubMed Central

Kekkonen, Mari; Hebert, Paul D N

2014-01-01

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

Bacillus Strains Most Closely Related to Bacillus nealsonii Are Not Effectively Circumscribed within the Taxonomic Species Definition

PubMed Central

Peak, K. Kealy; Duncan, Kathleen E.; Luna, Vicki A.; King, Debra S.; McCarthy, Peter J.; Cannons, Andrew C.

2011-01-01

Bacillus strains with >99.7% 16S rRNA gene sequence similarity were characterized with DNA:DNA hybridization, cellular fatty acid (CFA) analysis, and testing of 100 phenotypic traits. When paired with the most closely related type strain, percent DNA:DNA similarities (% S) for six Bacillus strains were all far below the recommended 70% threshold value for species circumscription with Bacillus nealsonii. An apparent genomic group of four Bacillus strain pairings with 94%–70% S was contradicted by the failure of the strains to cluster in CFA- and phenotype-based dendrograms as well as by their differentiation with 9–13 species level discriminators such as nitrate reduction, temperature range, and acid production from carbohydrates. The novel Bacillus strains were monophyletic and very closely related based on 16S rRNA gene sequence. Coherent genomic groups were not however supported by similarly organized phenotypic clusters. Therefore, the strains were not effectively circumscribed within the taxonomic species definition. PMID:22046187

Application of the Group Foliation Method to the Complex Monge-Ampère Equation

NASA Astrophysics Data System (ADS)

Nutku, Y.; Sheftel, M. B.

2001-04-01

We apply the method of group foliation to the complex Monge-Ampère equation ( CMA 2) to establish a regular framework for finding its non-invariant solutions. We employ an infinite symmetry subgroup of CMA 2 to produce a foliation of the solution space into orbits of solutions with respect to this group and a corresponding splitting of CMA 2 into an automorphic system and a resolvent system. We propose a new approach to group foliation which is based on the commutator algebra of operators of invariant differentiation. This algebra together with its Jacobi identities provides the commutator representation of the resolvent system.

The antiporter-like subunit constituent of the universal adaptor of complex I, group 4 membrane-bound [NiFe]-hydrogenases and related complexes.

PubMed

Batista, Ana P; Marreiros, Bruno C; Pereira, Manuela M

2013-05-01

We have recently investigated the long-recognized relationship between complex I and group 4 [NiFe] hydrogenases and we have established the so-called Energy-converting hydrogenase related (Ehr) complex as a new member of the family. We have also observed that four subunits, homologues to NuoB, D, H and L, are common to the members of the family. We have designated this common group of subunits the universal adaptor. Taking into account the similarity of the Na(+)/H(+) antiporter-like subunits of complex I (NuoL, NuoM and NuoN) and the unique structural characteristic of the long amphipathic α helix part of NuoL, the nature of the antiporter-like subunit of the universal adaptor was questioned. Thus, in this work we further explore the properties of the universal adaptor, investigating which antiporter-like subunit is part of the universal adaptor. We observe that the universal adaptor contains an antiporter-like subunit with a long amphipathic α helix, similar to NuoL. Consequently, the long helix is a common denominator that has been conserved in all members of the family. Such conservation surely reflects the key role of such helix in the energy transduction mechanism of this family of enzymes.

Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

PubMed

Serrao, Natasha R; Steinke, Dirk; Hanner, Robert H

2014-01-01

Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.

Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.

PubMed

Zhang, Wei; Liu, Yuanyuan; Warren, Alan; Xu, Henglong

2014-12-15

The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

N-heterocyclic carbene gold(I) and silver(I) complexes bearing functional groups for bio-conjugation

PubMed Central

Garner, Mary E.; Niu, Weijia; Chen, Xigao; Ghiviriga, Ion; Tan, Weihong; Veige, Adam S.

2015-01-01

This work describes several synthetic approaches to append organic functional groups to gold and silver N-heterocyclic carbene (NHC) complexes suitable for applications in biomolecule conjugation. Carboxylate appended NHC ligands (3) lead to unstable AuI complexes that convert into bis-NHC species (4). A benzyl protected carboxylate NHC-AuI complex 2 was synthesized but deprotection to produce the carboxylic acid functionality could not be achieved. A small library of new alkyne functionalized NHC proligands were synthesized and used for subsequent silver and gold metalation reactions. The alkyne appended NHC gold complex 13 readily react with benzyl azide in a copper catalyzed azide-alkyne cycloaddition reaction to form the triazole appended NHC gold complex 14. Cell cytotoxicity studies were performed on DLD-1 (colorectal adenocarcinoma), Hep-G2 (hepatocellular carcinoma), MCF-7 (breast adenocarcinoma), CCRF-CEM (human T-Cell leukemia), and HEK (human embryonic kidney). Complete spectroscopic characterization of the ligands and complexes was achieved using 1H and 13C NMR, gHMBC, ESI-MS, and combustion analysis. PMID:25490699

Developmental Antecedents of Taxonomic and Thematic Strategies at 3 Years of Age.

ERIC Educational Resources Information Center

Dunham, Philip; Dunham, Frances

1995-01-01

Individual differences in children's conceptual strategies at 3 years of age were predicted by aspects of children's behavior and language at 13 and 24 months. Production of pointing gestures at 13 months and nouns and attributive adjectives at 24 months were positively associated with the use of a taxonomic matching strategy at 3 years of age.…

Phylogeny and taxonomic revision of Thelonectria discophora (Ascomycota, Hypocreales, Nectriaceae) species complex

USDA-ARS?s Scientific Manuscript database

Thelonectria discophora (Thelonectria, Nectriaceae, Hypocreales) is a conspicuous group of saprobic fungi on decaying plant material, characterized by red perithecia each with a broad mammiform (nipple-like) apex. The anamorphic state is characterized by a cylindrocarpon-like morphology, with 3–5 se...

Metal–Metal Bonding in Uranium–Group 10 Complexes

PubMed Central

2016-01-01

Heterobimetallic complexes containing short uranium–group 10 metal bonds have been prepared from monometallic IUIV(OArP-κ2O,P)3 (2) {[ArPO]− = 2-tert-butyl-4-methyl-6-(diphenylphosphino)phenolate}. The U–M bond in IUIV(μ-OArP-1κ1O,2κ1P)3M0, M = Ni (3–Ni), Pd (3–Pd), and Pt (3–Pt), has been investigated by experimental and DFT computational methods. Comparisons of 3–Ni with two further U–Ni complexes XUIV(μ-OArP-1κ1O,2κ1P)3Ni0, X = Me3SiO (4) and F (5), was also possible via iodide substitution. All complexes were characterized by variable-temperature NMR spectroscopy, electrochemistry, and single crystal X-ray diffraction. The U–M bonds are significantly shorter than any other crystallographically characterized d–f-block bimetallic, even though the ligand flexes to allow a variable U–M separation. Excellent agreement is found between the experimental and computed structures for 3–Ni and 3–Pd. Natural population analysis and natural localized molecular orbital (NLMO) compositions indicate that U employs both 5f and 6d orbitals in covalent bonding to a significant extent. Quantum theory of atoms-in-molecules analysis reveals U–M bond critical point properties typical of metallic bonding and a larger delocalization index (bond order) for the less polar U–Ni bond than U–Pd. Electrochemical studies agree with the computational analyses and the X-ray structural data for the U–X adducts 3–Ni, 4, and 5. The data show a trend in uranium–metal bond strength that decreases from 3–Ni down to 3–Pt and suggest that exchanging the iodide for a fluoride strengthens the metal–metal bond. Despite short U–TM (transition metal) distances, four other computational approaches also suggest low U–TM bond orders, reflecting highly transition metal localized valence NLMOs. These are more so for 3–Pd than 3–Ni, consistent with slightly larger U–TM bond orders in the latter. Computational studies of the model systems (PH3)3MU(OH)3I

Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae).

PubMed

Janssen, Toon; Karssen, Gerrit; Orlando, Valeria; Subbotin, Sergei A; Bert, Wim

2017-12-01

Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus. Copyright © 2017 Elsevier Inc. All rights reserved.

Technetium-99m and rhenium-188 complexes with one and two pendant bisphosphonate groups for imaging arterial calcification.

PubMed

Bordoloi, Jayanta Kumar; Berry, David; Khan, Irfan Ullah; Sunassee, Kavitha; de Rosales, Rafael Torres Martin; Shanahan, Catherine; Blower, Philip J

2015-03-21

The first (99m)Tc and (188)Re complexes containing two pendant bisphosphonate groups have been synthesised, based on the mononuclear M(v) nitride core with two dithiocarbamate ligands each with a pendant bisphosphonate. The structural identity of the (99)Tc and stable rhenium analogues as uncharged, mononuclear nitridobis(dithiocarbamate) complexes was determined by electrospray mass spectrometry. The (99m)Tc complex showed greater affinity for synthetic and biological hydroxyapatite, and greater stability in biological media, than the well-known but poorly-characterised and inhomogeneous bone imaging agent (99m)Tc-MDP. It gave excellent SPECT images of both bone calcification (mice and rats) and vascular calcification (rat model), but the improved stability and the availability of two pendant bisphosphonate groups conferred no dramatic advantage in imaging over the conventional (99m)Tc-MDP agent in which the bisphosphonate group is bound directly to Tc. The (188)Re complex also showed preferential uptake in bone. These tracers and the biological model of vascular calcification offer the opportunity to study the biological interpretation and clinical potential of radionuclide imaging of vascular calcification and to deliver radionuclide therapy to bone metastases.

Taxonomic revision and molecular phylogenetics of the Idarnes incertus species-group (Hymenoptera, Agaonidae, Sycophaginae)

PubMed Central

Cruaud, Astrid; Genson, Gwenaëlle; Rasplus, Jean-Yves; Pereira, Rodrigo A.S.

2017-01-01

Sycophaginae is a group of non-pollinating fig wasps considered closely related to the fig pollinators (Agaoninae, Tetrapusiinae, and Kradibiinae) in the most recent phylogenetic analyses. They occur in all tropical regions and are associated with Ficus subgenera Urostigma and Sycomorus. There are six described genera of Sycophaginae, and two are native and confined to the Neotropics, namely Idarnes Walker, 1843 and Anidarnes Bouček, 1993. Genus Idarnes is divided into three morphologically distinct groups that were proven to be monophyletic by recent molecular phylogenetic analyses. In this paper we reviewed the Idarnes incertus species-group and provide detailed morphological descriptions and illustrations for the species belonging to this group. Three previously described species were redescribed: I. brasiliensis (Mayr, 1906) comb. nov., I. hansoni Bouček, 1993, and I. incertus (Ashmead, 1900). Seventeen new species are described by Farache and Rasplus: I. amacayacuensis sp. n., I. amazonicus sp. n., I. americanae sp. n., I. badiovertex sp. n., I. brevis sp. n., I. brunneus sp. n., I. comptoni sp. n., I. cremersiae sp. n., I. dimorphicus sp. n., I. flavicrus sp. n., I. flaviventris sp. n., I. gibberosus sp. n., I. gordhi sp. n., I. maximus sp. n., I. nigriventris sp. n., I. pseudoflavus sp. n. and I. ramirezi sp. n. We provided keys for the identification of the species as well as for recognising the different species-groups of Idarnes and a closely related genus (Sycophaga Westwood, 1840). Additionally, phylogenetic relationships among 13 species of the I. incertus species-group were inferred using four molecular markers and discussed in the light of Ficus taxonomy and host specificity. PMID:28168097

Determinants and taxonomic consequences of extreme egg shell variability in Ramazzottius subanomalus (Biserov, 1985) (Tardigrada).

PubMed

Stec, Daniel; Morek, Witold; Gąsiorek, Piotr; Kaczmarek, Łukasz; Michalczyk, Łukasz

2016-12-15

Nearly a half of known eutardigrade species lay ornamented eggs. The ornamentation is thought to provide attachment of the egg to the substrate and protection for the developing embryo, but from the taxonomic point of view chorion morphology may also provide key characters for species differentiation and identification, especially between closely related taxa. Nonetheless, despite the evolutionary and taxonomic importance of the egg shell, the determinants of its morphology are very poorly, if at all, understood. Here, we combine morphological, molecular and experimental approaches in an attempt to separate the genetic and environmental factors that shape egg chorion morphology in Ramazzottius subanomalus (Biserov, 1985). Our integrative study, based on a population of R. subanomalus isolated from a single moss sample, revealed (1) remarkable variation in egg shell morphology, but (2) relatively little variation in animal morphometric traits, and (3) genetic differentiation, expressed as two ITS-2 haplotypes, but no parallel polymorphism in COI. Although animals did not differ morphometrically between the haplotypes, eggs laid by haplotype 1 and 2 females exhibited highly statistically significant differences in all measured traits. The study demonstrates, for the first time, a correlation between phenotypic and genetic variability within a tardigrade species. The revealed congruence between genetic and morphological traits might be viewed as an example of incipient speciation that illustrates early evolutionary steps leading to species complexes that differ primarily in terms of egg shell morphology. Moreover, our data confirm the value of the ITS-2 fragment in distinguishing very closely related tardigrade lineages.

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

USDA-ARS?s Scientific Manuscript database

Community composition data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alt...

A Mathematical Framework for the Complex System Approach to Group Dynamics: The Case of Recovery House Social Integration.

PubMed

Light, John M; Jason, Leonard A; Stevens, Edward B; Callahan, Sarah; Stone, Ariel

2016-03-01

The complex system conception of group social dynamics often involves not only changing individual characteristics, but also changing within-group relationships. Recent advances in stochastic dynamic network modeling allow these interdependencies to be modeled from data. This methodology is discussed within a context of other mathematical and statistical approaches that have been or could be applied to study the temporal evolution of relationships and behaviors within small- to medium-sized groups. An example model is presented, based on a pilot study of five Oxford House recovery homes, sober living environments for individuals following release from acute substance abuse treatment. This model demonstrates how dynamic network modeling can be applied to such systems, examines and discusses several options for pooling, and shows how results are interpreted in line with complex system concepts. Results suggest that this approach (a) is a credible modeling framework for studying group dynamics even with limited data, (b) improves upon the most common alternatives, and (c) is especially well-suited to complex system conceptions. Continuing improvements in stochastic models and associated software may finally lead to mainstream use of these techniques for the study of group dynamics, a shift already occurring in related fields of behavioral science.

A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.

PubMed

Yu, J; Blom, J; Glaeser, S P; Jaenicke, S; Juhre, T; Rupp, O; Schwengers, O; Spänig, S; Goesmann, A

2017-11-10

The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Influence of a Heterocyclic Nitrogen-Donor Group on the Coordination of Trivalent Actinides and Lanthanides by Aminopolycarboxylate Complexants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimes, Travis S.; Heathman, Colt R.; Jansone-Popova, Santa

Here, the novel metal chelator N-2-(pyridylmethyl)diethylenetriamine- N,N',N",N"-tetraacetic acid (DTTA-PyM) was designed to replace a single oxygen-donor acetate group of the well-known aminopolycarboxylate complexant diethylenetriamine- N,N,N',N",N"-pentaacetic acid (DTPA) with a nitrogen-donor 2-pyridylmethyl. Potentiometric, spectroscopic, computational, and radioisotope distribution methods show distinct differences for the 4f and 5f coordination environments and enhanced actinide binding due to the nitrogen-bearing heterocyclic moiety. The Am 3+, Cm 3+, and Ln 3+ complexation studies for DTTA-PyM reveal an enhanced preference, relative to DTPA, for trivalent actinide binding. Fluorescence studies indicate no changes to the octadentate coordination of trivalent curium, while evidence of heptadentate complexation of trivalentmore » europium is found in mixtures containing EuHL (aq) complexes at the same aqueous acidity. The denticity change observed for Eu 3+ suggests that complex protonation occurs on the pyridyl nitrogen. Formation of the CmHL (aq) complex is likely due to the protonation of an available carboxylate group because the carbonyl oxygen can maintain octadentate coordination through a rotation. The observed suppressed protonation of the pyridyl nitrogen in the curium complexes may be attributed to stronger trivalent actinide binding by DTTA-PyM. Density functional theory calculations indicate that added stabilization of the actinide complexes with DTTA-PyM may originate from π-back-bonding interactions between singly occupied 5f orbitals of Am 3+ and the pyridyl nitrogen. The differences between the stabilities of trivalent actinide chelates (Am 3+, Cm 3+) and trivalent lanthanide chelates (La 3+–Lu 3+) are observed in liquid–liquid extraction systems, yielding unprecedented 4f/5f differentiation when using DTTA-PyM as an aqueous holdback reagent. In addition, the enhanced nitrogen-donor softness of the new DTTA-PyM chelator was perturbed

Evolutionary dynamics of taxonomic structure

PubMed Central

Foote, Michael

2012-01-01

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

A distinct species, Dodona formosana, detected in the Dodona eugenes species complex: clarification of the taxonomic status of the Punch butterfly in Taiwan

PubMed Central

Wu, Li-Wei; Lin, Wen-Jie; Hsu, Yu-Feng

2018-01-01

Abstract The Tailed Punch, Dodona eugenes, is widely distributed in East Asia with seven subspecies currently recognized. However, two of them, namely ssp. formosana and ssp. esakii found in Taiwan, are hard to distinguish from each other due to ambiguous diagnostic characters. In this study, their taxonomic status is clarified by comparing genitalia characters and phylogenetic relationships based on mitochondrial sequences, COI and COII (total 2211 bps). Our results show that there is no reliable feature to separate these two subspecies. Surprisingly we found that Dodona in Taiwan is more closely related to the Orange Punch, D. egeon, than to other subspecies of D. eugenes. Therefore, the following nomenclatural changes are proposed: Dodona eugenes formosana is revised to specific status as Dodona formosana Matsumura, 1919, stat. rev, and ssp. esakii is sunk to a junior synonym of Dodona formosana syn. n. PMID:29674868

Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

PubMed

Wang, Q-M; Begerow, D; Groenewald, M; Liu, X-Z; Theelen, B; Bai, F-Y; Boekhout, T

2015-06-01

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, Angela L.; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

PubMed

Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

2016-08-18

Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

Integrative taxonomy of the fly orchid group: insights from chemical ecology

NASA Astrophysics Data System (ADS)

Joffard, Nina; Buatois, Bruno; Schatz, Bertrand

2016-10-01

Several authors have recently stressed the need to develop an integrative approach in taxonomy, but studies applying such an approach to Mediterranean orchids are scarce. In sexually deceptive orchids from the taxonomically difficult genus Ophrys, pollination is specific and performed by male insects attracted to the flowers by sex pheromone-mimicking floral scents. Floral compounds are therefore of primary importance for reproductive isolation and species delimitations in this genus. In the fly orchid group, molecular, morphological, and ecological characters have been extensively studied, but a comprehensive survey of floral scents is still lacking. In the present study, the blends of floral compounds of its three members, Ophrys insectifera, Ophrys aymoninii, and Ophrys subinsectifera, were extracted and analyzed by gas chromatography-mass spectrometry. A total of 107 compounds were found, with a majority of saturated and unsaturated hydrocarbons. Significant differentiation, both qualitative and quantitative, was found among the three taxa. This result, pooled with those from the literature, forms a comprehensive and congruent dataset that allows us to elucidate the taxonomic rank of the three members of the fly orchid group.

Integrative taxonomy: Combining morphological, molecular and chemical data for species delineation in the parthenogenetic Trhypochthonius tectorum complex (Acari, Oribatida, Trhypochthoniidae)

PubMed Central

2011-01-01

Background There is a long-standing controversial about how parthenogenetic species can be defined in absence of a generally accepted species concept for this reproductive mode. An integrative approach was suggested, combining molecular and morphological data to identify distinct monophyletic entities. Using this approach, speciation of parthenogenetic lineages was recently demonstrated for groups of bdelloid rotifers and oribatid mites. Trhypochthonius tectorum, an oribatid mite from the entirely parthenogenetic desmonomatan family Trhypochthoniidae, is traditionally treated as a single species in Central Europe. However, two new morphological lineages were recently proposed for some Austrian populations of T. tectorum, and were described as novel subspecies (T. silvestris europaeus) or form (T. japonicus forma occidentalis). We used the morphological and morphometrical data which led to this separation, and added mitochondrial and nuclear DNA sequences and the chemical composition of complex exocrine oil gland secretions to test this taxonomical hypothesis. This is the first attempt to combine these three types of data for integrative taxonomical investigations of oribatid mites. Results We show that the previous European species T. tectorum represents a species complex consisting of three distinct lineages in Austria (T.tectorum, T. silvestris europaeus and T. japonicus forma occidentalis), each clearly separated by morphology, oil gland secretion profiles and mitochondrial cox1 sequences. This diversification happened in the last ten million years. In contrast to these results, no variation among the lineages was found in the nuclear 18S rDNA. Conclusions Our approach combined morphological, molecular and chemical data to investigate diversity and species delineation in a parthenogenetic oribatid mite species complex. To date, hypotheses of a general oribatid mite phylogeny are manifold, and mostly based on single-method approaches. Probably, the integrative

Deaf and Hard of Hearing Adolescents' Processing of Pictures and Written Words for Taxonomic Categories in a Priming Task of Semantic Categorization

ERIC Educational Resources Information Center

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written…

Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard.

PubMed

Hacking, Jessica; Bertozzi, Terry; Moussalli, Adnan; Bradford, Tessa; Gardner, Michael

2018-07-01

Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region. Copyright © 2018 Elsevier Ltd. All rights reserved.

An integrated approach to the Taxonomic identification of prehistoric shell ornaments

USGS Publications Warehouse

Demarchi, Beatrice; O'Connor, Sonia; Ponzoni, Andre de Lima; Ponzoni, Raquel de Almeida Roch; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

2014-01-01

Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.

Study of the Moraxella group. I. Genus Moraxella and the Neisseria catarrhalis group.

PubMed

Baumann, P; Doudoroff, M; Stanier, R Y

1968-01-01

A number of strains of oxidase-positive moraxellas and of neisserias related to Neisseria catarrhalis were characterized with respect to a number of nutritional and physiological properties and could be assigned to several species or species groups on the basis of their phenotypic traits. This grouping was consistent with that established by Bövre on the basis of transformation frequencies for streptomycin resistance. It is proposed to reserve the generic name Moraxella for the oxidase-positive rodshaped organisms, and a redescription of the genus is offered. Following the recent taxonomic proposals of Bövre and Henriksen, the specific name Moraxella osloensis is applied to the nutritionally unexacting strains that accumulate poly-beta-hydroxybutyrate as carbon reserve. The nutritionally exacting strains are assigned to three distinct groups which can be regarded as separate species or as varieties of M. lacunata. The epithets applicable to these groups appear to be lacunata, nonliquefaciens, and bovis. The "false neisserias" could be assigned to at least three subgroups, one of which constitutes the clearly defined entity, N. catarrhalis, which could be distinguished from N. caviae and N. ovis.

The hyper-diverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in the Malagasy region taxonomic revision of the T. naganum, T. plesiarum, T. schaufussii, and T. severini species groups

PubMed Central

Hita Garcia, Francisco; Fisher, Brian L.

2014-01-01

Abstract The taxonomy of the Tetramorium naganum, T. plesiarum, T. schaufussii, and T. severini species groups are revised for the Malagasy region. A total of 31 species are treated, of which 22 are newly described and nine redescribed. This increases the richness of the hyper-diverse genus Tetramorium in the Malagasy region to 106 species, which makes it the most species-rich genus in the region. Twenty-nine of the treated species are endemic to Madagascar, one is endemic to the Comoros, and one species is found predominantly in Madagascar but also on the island of Reunion. The T. naganum species group contains five species, which are mainly distributed in the rainforests and montane rainforests of eastern and northern Madagascar: T. alperti sp. n., T. dalek sp. n., T. enkidu sp. n., T. gilgamesh sp. n., and T. naganum Bolton, 1979. The T. plesiarum species group holds five species: T. bressleri sp. n., T. hobbit sp. n., T. gollum sp. n., T. mars sp. n., and T. plesiarum Bolton, 1979. All five are arid-adapted species occurring in the southwest and west of Madagascar. The second-most species-rich group in the region is the T. schaufussii species group with 20 species, most of which inhabit rainforests or montane rainforests of eastern and northern Madagascar. This group includes two species complexes each containing ten species: the T. cognatum complex with the species T. aspis sp. n., T. camelliae sp. n., T. cognatum Bolton, 1979, T. freya sp. n., T. gladius sp. n., T. karthala sp. n., T. myrmidon sp. n., T. proximum Bolton, 1979, T. rumo sp. n., and T. tenuinode sp. n.; and the T. schaufussii complex with the species T. merina sp. n., T. monticola sp. n., T. nassonowii Forel, 1892 stat. n., T. obiwan sp. n., T. pseudogladius sp. n., T. rala sp. n., T. schaufussii Forel, 1891, T. sikorae Forel, 1892 (= T. latior (Santschi, 1926)), T. scutum sp. n., T. xanthogaster Santschi, 1911. The last group treated in this study is the T. severini species group, which

The Human Polycomb Group Complex Associates with Pericentromeric Heterochromatin to Form a Novel Nuclear Domain

PubMed Central

Saurin, Andrew J.; Shiels, Carol; Williamson, Jill; Satijn, David P.E.; Otte, Arie P.; Sheer, Denise; Freemont, Paul S.

1998-01-01

The Polycomb group (PcG) complex is a chromatin-associated multiprotein complex, involved in the stable repression of homeotic gene activity in Drosophila. Recently, a mammalian PcG complex has been identified with several PcG proteins implicated in the regulation of Hox gene expression. Although the mammalian PcG complex appears analogous to the complex in Drosophila, the molecular mechanisms and functions for the mammalian PcG complex remain unknown. Here we describe a detailed characterization of the human PcG complex in terms of cellular localization and chromosomal association. By using antibodies that specifically recognize three human PcG proteins— RING1, BMI1, and hPc2—we demonstrate in a number of human cell lines that the PcG complex forms a unique discrete nuclear structure that we term PcG bodies. PcG bodies are prominent novel nuclear structures with the larger PcG foci generally localized near the centromeres, as visualized with a kinetochore antibody marker. In both normal fetal and adult fibroblasts, PcG bodies are not randomly dispersed, but appear clustered into defined areas within the nucleus. We show in three different human cell lines that the PcG complex can tightly associate with large pericentromeric heterochromatin regions (1q12) on chromosome 1, and with related pericentromeric sequences on different chromosomes, providing evidence for a mammalian PcG–heterochromatin association. Furthermore, these heterochromatin-bound PcG complexes remain stably associated throughout mitosis, thereby allowing the potential inheritance of the PcG complex through successive cell divisions. We discuss these results in terms of the known function of the PcG complex as a transcriptional repression complex. PMID:9722603

A taxonomic review of the Neoserica (sensu lato) septemlamellata group (Coleoptera, Scarabaeidae, Sericini)

PubMed Central

Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

2014-01-01

Abstract In the present paper the species belonging to the Neoserica (sensu lato) septemlamellata group, that included so far only four known species, are revised. Here we describe eleven new species originating mainly from Indochina and Southern China: N. daweishanica sp. n., N. gaoligongshanica sp. n., N. guangpingensis sp. n., N. igori sp. n., N. jiulongensis sp. n., N. plurilamellata sp. n., N. weishanica sp. n., N. yanzigouensis sp. n. (China) N. sapaensis sp. n. (China, Vietnam), N. bansongchana sp. n., N. takakuwai sp. n. (Laos). The lectotypes of Neoserica septemlamellata Brenske, 1898 and N. septemfoliata Moser, 1915 are designated. Keys to the species and species groups are given, the genitalia of all species and their habitus are illustrated and distribution maps are included. PMID:24843263

Taxonomic etymology – in search of inspiration

PubMed Central

Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

2015-01-01

Abstract We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common – given after morphological features – through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons), science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names. PMID:26257573

CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

EPA Science Inventory

We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

Taxonomic revision of New Guinea diving beetles of the Exocelina danae group, with the description of ten new species (Coleoptera, Dytiscidae, Copelatinae)

PubMed Central

Shaverdo, Helena; Sagata, Katayo; Balke, Michael

2016-01-01

Abstract Ten new species of Exocelina Broun, 1886 from New Guinea are described: Exocelina andakombensis sp. n., Exocelina garaina sp. n., Exocelina injiensis sp. n., Exocelina kabwumensis sp. n., Exocelina marawaga sp. n., Exocelina posmani sp. n., Exocelina tekadu sp. n., Exocelina varirata sp. n., Exocelina wareaga sp. n., and Exocelina woitapensis sp. n. All of them together with five already described species are united into the newly defined Exocelina danae-group (with Exocelina miriae-subgroup), a polyphyletic complex of related species with lateral setation on the median lobe. In the light of newly available material, all previously described species of the Exocelina rivulus-group are considered to belong to a single species, Exocelina damantiensis (Balke, 1998), which is now placed into the Exocelina danae-group, and three new synonyms are therefore proposed: Exocelina madangensis (Balke, 2001) syn. n., Exocelina patepensis (Balke, 1998) syn. n., and Exocelina rivulus (Balke, 1998) syn. n. Exocelina tarmluensis (Balke, 1998) syn. n. is a junior synonym of Exocelina danae (Balke, 1998). Redescription of Exocelina atratus (Balfour-Browne, 1939) is provided based on its type material. An identification key to all known species of the group is provided, and important diagnostic characters are illustrated. Data on the species distribution are given, showing that whilst most species are local endemics, Exocelina damantiensis is extremely widely distributed. PMID:27829789

Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice.

PubMed

Vas, Zoltán; Lefebvre, Louis; Johnson, Kevin P; Reiczigel, Jeno; Rózsa, Lajos

2011-10-01

Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon. Copyright © 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

On the Hodge-type decomposition and cohomology groups of k-Cauchy-Fueter complexes over domains in the quaternionic space

NASA Astrophysics Data System (ADS)

Chang, Der-Chen; Markina, Irina; Wang, Wei

2016-09-01

The k-Cauchy-Fueter operator D0(k) on one dimensional quaternionic space H is the Euclidean version of spin k / 2 massless field operator on the Minkowski space in physics. The k-Cauchy-Fueter equation for k ≥ 2 is overdetermined and its compatibility condition is given by the k-Cauchy-Fueter complex. In quaternionic analysis, these complexes play the role of Dolbeault complex in several complex variables. We prove that a natural boundary value problem associated to this complex is regular. Then by using the theory of regular boundary value problems, we show the Hodge-type orthogonal decomposition, and the fact that the non-homogeneous k-Cauchy-Fueter equation D0(k) u = f on a smooth domain Ω in H is solvable if and only if f satisfies the compatibility condition and is orthogonal to the set ℋ(k)1 (Ω) of Hodge-type elements. This set is isomorphic to the first cohomology group of the k-Cauchy-Fueter complex over Ω, which is finite dimensional, while the second cohomology group is always trivial.

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

PubMed Central

Le, Huong T.; Ho, Cuong T.; Trinh, Quan H.; Trinh, Duc A.; Luu, Minh T. N.; Tran, Hai S.; Orange, Didier; Janeau, Jean L.; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

2016-01-01

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

PubMed

Le, Huong T; Ho, Cuong T; Trinh, Quan H; Trinh, Duc A; Luu, Minh T N; Tran, Hai S; Orange, Didier; Janeau, Jean L; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

2016-01-01

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

[The effect of a short-term group stabilisation training in patients with complex posttraumatic stress disorder].

PubMed

Beldman, G; Kessels, H H L M; de Groot, I W

The international guideline for complex posttraumatic stress disorder (ptsd) from the International Society for Traumatic Stress Studies (istss) recommends treatment in phases, starting with stabilisation treatment. Different forms of stabilisation training have been developed the past few years, one being short-term group stabilisation training.
AIM: To map out the effects of the short-term group training.
METHOD: The research implemented a pre-post design. The training consisted of five group sessions. Questionnaires (bsi, OQ 45 and svl-15) were completed both prior to and after the training. Four domains were assessed: psychosymptomatology in general, depressive symptoms, problems with interpersonal functioning and ptsd-related symptoms. The effect of the training was calculated by paired t-tests.
RESULTS: The questionnaires of the 47 participants who had completed the training were analysed. No significant decrease was observed during the stabilisation training concerning the symptoms of the four evaluated domains.
CONCLUSION: Contrary our expectations, a short-term group-based stabilisation training does not seem to have added value when treating patients with complex ptsd. The results correspond with a recent trend in which the effectiveness of other stabilising methods is questioned. Alternative treatment options are discussed.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

PubMed

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-05-19

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

PubMed

Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

2018-04-01

Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

Taxonomic composition and physiological and biochemical properties of bacteria in the digestive tracts of earthworms

NASA Astrophysics Data System (ADS)

Byzov, B. A.; Tikhonov, V. V.; Nechitailo, T. Yu.; Demin, V. V.; Zvyagintsev, D. G.

2015-03-01

Several hundred bacterial strains belonging to different taxa were isolated and identified from the digestive tracts of soil and compost earthworms. Some physiological and biochemical properties of the bacteria were characterized. The majority of intestinal bacteria in the earthworms were found to be facultative anaerobes. The intestinal isolates as compared to the soil ones had elevated activity of proteases and dehydrogenases. In addition, bacteria associated with earthworms' intestines are capable of growth on humic acids as a sole carbon source. Humic acid stimulated the growth of the intestinal bacteria to a greater extent than those of the soil ones. In the digestive tracts, polyphenol oxidase activity was found. Along with the data on the taxonomic separation of the intestinal bacteria, the features described testified to the presence of a group of bacteria in the earthworms intestines that is functionally characteristic and is different from the soil bacteria.

Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

PubMed

Zhou, Li-Wei; Cao, Yun; Wu, Sheng-Hua; Vlasák, Josef; Li, De-Wei; Li, Meng-Jie; Dai, Yu-Cheng

2015-06-01

Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Neurocomputational Account of Taxonomic Responding and Fast Mapping in Early Word Learning

ERIC Educational Resources Information Center

Mayor, Julien; Plunkett, Kim

2010-01-01

We present a neurocomputational model with self-organizing maps that accounts for the emergence of taxonomic responding and fast mapping in early word learning, as well as a rapid increase in the rate of acquisition of words observed in late infancy. The quality and efficiency of generalization of word-object associations is directly related to…

Group 6 metal pentacarbonyl complexes of air-stable primary, secondary, and tertiary ferrocenylethylphosphines.

PubMed

Rabiee Kenaree, Amir; Sauvé, Ethan R; Ragogna, Paul J; Gilroy, Joe B

2016-02-21

The synthesis and characterization of a series of Group 6 metal pentacarbonyl complexes of air stable primary, secondary, and tertiary phosphines containing ferrocenylethyl substituents are reported [M(CO)5L: M = Cr, Mo, W; L = PH2(CH2CH2Fc), PH(CH2CH2Fc)2, P(CH2CH2Fc)3]. The structure and composition of the complexes were confirmed by multinuclear NMR spectroscopy, IR and UV-Vis absorption spectroscopy, mass spectrometry, X-ray crystallography, and elemental analysis. The solid-state structural data reported revealed trends in M-C and M-P bond lengths that mirrored those of the atomic radii of the Group 6 metals involved. UV-Vis absorption spectroscopy and cyclic voltammetry highlighted characteristics consistent with electronically isolated ferrocene units including wavelengths of maximum absorption between 435 and 441 nm and reversible one-electron (per ferrocene unit) oxidation waves between 10 and -5 mV relative to the ferrocene/ferrocenium redox couple. IR spectroscopy confirmed that the σ donating ability of the phosphines increased as ferrocenylethyl substituents were introduced and that the tertiary phosphine ligand described is a stronger σ donor than PPh3 and a weaker σ donor than PEt3, respectively.

Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.

PubMed

Tanner, Kristie; Martí, Jose Manuel; Belliure, Josabel; Fernández-Méndez, Mar; Molina-Menor, Esther; Peretó, Juli; Porcar, Manuel

2018-02-01

Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Structure of the Human Centrin 2-Xeroderma Pigmentosum Group C Protein Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson,J.; Ryan, Z.; Salisbury, J.

2006-01-01

Human centrin-2 plays a key role in centrosome function and stimulates nucleotide excision repair by binding to the xeroderma pigmentosum group C protein. To determine the structure of human centrin-2 and to develop an understanding of molecular interactions between centrin and xeroderma pigmentosum group C protein, we characterized the crystal structure of calcium-loaded full-length centrin-2 complexed with a xeroderma pigmentosum group C peptide. Our structure shows that the carboxyl-terminal domain of centrin-2 binds this peptide and two calcium atoms, whereas the amino-terminal lobe is in a closed conformation positioned distantly by an ordered {alpha}-helical linker. A stretch of the amino-terminalmore » domain unique to centrins appears disordered. Two xeroderma pigmentosum group C peptides both bound to centrin-2 also interact to form an {alpha}-helical coiled-coil. The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin.« less

Synthesis and Biological Evaluation of Ru(II) and Pt(II) Complexes Bearing Carboxyl Groups as Potential Anticancer Targeted Drugs.

PubMed

Martínez, Ma Ángeles; Carranza, M Pilar; Massaguer, Anna; Santos, Lucia; Organero, Juan A; Aliende, Cristina; de Llorens, Rafael; Ng-Choi, Iteng; Feliu, Lidia; Planas, Marta; Rodríguez, Ana M; Manzano, Blanca R; Espino, Gustavo; Jalón, Félix A

2017-11-20

The synthesis and characterization of Pt(II) (1 and 2) and Ru(II) arene (3 and 4) or polypyridine (5 and 6) complexes is described. With the aim of having a functional group to form bioconjugates, one uncoordinated carboxyl group has been introduced in all complexes. Some of the complexes were selected for their potential in photodynamic therapy (PDT). The molecular structures of complexes 2 and 5, as well as that of the sodium salt of the 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine ligand (cptpy), were determined by X-ray diffraction. Different techniques were used to evaluate the binding capacity to model DNA molecules, and MTT cytotoxicity assays were performed against four cell lines. Compounds 3, 4, and 5 showed little tendency to bind to DNA and exhibited poor biological activity. Compound 2 behaves as bonded to DNA probably through a covalent interaction, although its cytotoxicity was very low. Compound 1 and possibly 6, both of which contain a cptpy ligand, were able to intercalate with DNA, but toxicity was not observed for 6. However, compound 1 was active in all cell lines tested. Clonogenic assays and apoptosis induction studies were also performed on the PC-3 line for 1. The photodynamic behavior for complexes 1, 5, and 6 indicated that their nuclease activity was enhanced after irradiation at λ = 447 nm. The cell viability was significantly reduced only in the case of 5. The different behavior in the absence or presence of light makes complex 5 a potential prodrug of interest in PDT. Molecular docking studies followed by molecular dynamics simulations for 1 and the counterpart without the carboxyl group confirmed the experimental data that pointed to an intercalation mechanism. The cytotoxicity of 1 and the potential of 5 in PDT make them good candidates for subsequent conjugation, through the carboxyl group, to "selected peptides" which could facilitate the selective vectorization of the complex toward receptors that are overexpressed in

Coral identity underpins architectural complexity on Caribbean reefs.

PubMed

Alvarez-Filip, Lorenzo; Dulvy, Nicholas K; Côte, Isabelle M; Watkinson, Andrew R; Gill, Jennifer A

2011-09-01

The architectural complexity of ecosystems can greatly influence their capacity to support biodiversity and deliver ecosystem services. Understanding the components underlying this complexity can aid the development of effective strategies for ecosystem conservation. Caribbean coral reefs support and protect millions of livelihoods, but recent anthropogenic change is shifting communities toward reefs dominated by stress-resistant coral species, which are often less architecturally complex. With the regionwide decline in reef fish abundance, it is becoming increasingly important to understand changes in coral reef community structure and function. We quantify the influence of coral composition, diversity, and morpho-functional traits on the architectural complexity of reefs across 91 sites at Cozumel, Mexico. Although reef architectural complexity increases with coral cover and species richness, it is highest on sites that are low in taxonomic evenness and dominated by morpho-functionally important, reef-building coral genera, particularly Montastraea. Sites with similar coral community composition also tend to occur on reefs with very similar architectural complexity, suggesting that reef structure tends to be determined by the same key species across sites. Our findings provide support for prioritizing and protecting particular reef types, especially those dominated by key reef-building corals, in order to enhance reef complexity.

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Interactive effects of chemical and biological controls on food-web composition in saline prairie lakes.

PubMed

Cooper, Ryan N; Wissel, Björn

2012-11-27

Salinity is restricting habitatability for many biota in prairie lakes due to limited physiological abilities to cope with increasing osmotic stress. Yet, it remains unclear how salinity effects vary among major taxonomic groups and what role other environmental parameters play in shaping food-web composition. To answer these questions, we sampled fish, zooplankton and littoral macroinvertebrates in 20 prairie lakes (Saskatchewan, Canada) characterized by large gradients in water chemistry and lake morphometry. We showed that salinity thresholds differed among major taxonomic groups, as most fishes were absent above salinities of 2 g L-1, while littoral macroinvertebrates were ubiquitous. Zooplankton occurred over the whole salinity range, but changed taxonomic composition as salinity increased. Subsequently, the complexity of fish community (diversity) was associated with large changes in invertebrate communities. The directional changes in invertebrate communities to smaller taxa indicated that complex fish assemblages resulted in higher predation pressure. Most likely, as the complexity of fish community decreased, controls of invertebrate assemblages shifted from predation to competition and ultimately to productivity in hypersaline lakes. Surprisingly, invertebrate predators did not thrive in the absence of fishes in these systems. Furthermore, the here identified salinity threshold for fishes was too low to be a result of osmotic stress. Hence, winterkill was likely an important factor eliminating fishes in low salinity lakes that had high productivity and shallow water depth. Ultimately, while salinity was crucial, intricate combinations of chemical and biological mechanisms also played a major role in controlling the assemblages of major taxonomic groups in prairie lakes.

Interactive effects of chemical and biological controls on food-web composition in saline prairie lakes

PubMed Central

2012-01-01

Salinity is restricting habitatability for many biota in prairie lakes due to limited physiological abilities to cope with increasing osmotic stress. Yet, it remains unclear how salinity effects vary among major taxonomic groups and what role other environmental parameters play in shaping food-web composition. To answer these questions, we sampled fish, zooplankton and littoral macroinvertebrates in 20 prairie lakes (Saskatchewan, Canada) characterized by large gradients in water chemistry and lake morphometry. We showed that salinity thresholds differed among major taxonomic groups, as most fishes were absent above salinities of 2 g L-1, while littoral macroinvertebrates were ubiquitous. Zooplankton occurred over the whole salinity range, but changed taxonomic composition as salinity increased. Subsequently, the complexity of fish community (diversity) was associated with large changes in invertebrate communities. The directional changes in invertebrate communities to smaller taxa indicated that complex fish assemblages resulted in higher predation pressure. Most likely, as the complexity of fish community decreased, controls of invertebrate assemblages shifted from predation to competition and ultimately to productivity in hypersaline lakes. Surprisingly, invertebrate predators did not thrive in the absence of fishes in these systems. Furthermore, the here identified salinity threshold for fishes was too low to be a result of osmotic stress. Hence, winterkill was likely an important factor eliminating fishes in low salinity lakes that had high productivity and shallow water depth. Ultimately, while salinity was crucial, intricate combinations of chemical and biological mechanisms also played a major role in controlling the assemblages of major taxonomic groups in prairie lakes. PMID:23186395

Taxonomic and functional distinctness of the fish assemblages in three coastal environments (bays, coastal lagoons and oceanic beaches) in Southeastern Brazil.

PubMed

Azevedo, Márcia Cristina Costa; Gomes-Gonçalves, Rafaela de Sousa; Mattos, Tailan Moretti; Uehara, Wagner; Guedes, Gustavo Henrique Soares; Araújo, Francisco Gerson

2017-08-01

Several species of marine fish use different coastal systems especially during their early development. However, these habitats are jeopardized by anthropogenic influences threatening the success of fish populations, and urgent measures are needed to priorize areas to protect their sustainability. We applied taxonomic (Δ+) and functional (X+) distinctiveness indices that represent taxonomic composition and functional roles to assess biodiversity of three different costal systems: bays, coastal lagoons and oceanic beaches. We hypothesized that difference in habitat characteristics, especially in the more dynamism and habitat homogeneity of oceanic beaches compared with more habitat diversity and sheltered conditions of bays and coastal lagoons results in differences in fish richness and taxonomic and functional diversity. The main premise is that communities phylogenetically and functionally more distinct have more interest in conservation policies. Significant differences (P < 0.004) were found in the species richness, Δ+ and X+ among the three systems according to PERMANOVA. Fish richness was higher in bays compared with the coastal lagoons and oceanic beaches. Higher Δ+ was found for the coastal lagoons compared with the bays and oceanic beaches, with the bays having some values below the confidence limit. Similar patterns were found for X+, although all values were within the confidence limits for the bays, suggesting that the absence of some taxa does not interfere in functional diversity. The hypothesis that taxonomic and functional structure of fish assemblages differ among the three systems was accepted and we suggest that coastal lagoons should be priorized in conservation programs because they support more taxonomic and functional distinctiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Taxonomic and nontaxonomic responses to ecological changes in an urban lowland stream through the use of Chironomidae (Diptera) larvae.

PubMed

Cortelezzi, A; Paggi, A C; Rodríguez, M; Capítulo, A Rodrigues

2011-03-01

Biotic descriptors--both taxonomic (diversity indices, species richness, and indicator species) and nontaxonomic (biomass, oxygen consumption/production, and anatomical deformities)--are useful tools for measuring a stream's ecological condition. Nontaxonomic parameters detect critical effects not reflected taxonomically. We analyzed changes in Chironomidae populations as taxonomic parameters and mentum deformities as a nontaxonomic parameter for evaluating a South-American-plains stream (Argentina). We performed samplings seasonally (March, June, September, and December; 2005) and physical and chemical measurements at three sampling sites of the stream (DC1 at river source, through DC3 downstream). The specimens collected in sediment and vegetation were analyzed to investigate mouth deformities in Chironomidae larvae. We identified a total of 9 taxa from Chironomidae and Orthocladiinae subfamilies. Shannon's diversity index for Chironomidae decreased from 1.6 bits ind⁻¹ (DC1) to 0.3 bits ind⁻¹ (DC3). The total density of the Chironomidae exhibited a great increase in abundance at site DC3, especially that of Chironomus calligraphus. Chironomidae taxonomic composition also changed among the three sites despite their spatial proximity: C. calligraphus, Goeldichironomus holoprasinus, Parachironomus longistilus, and Polypedilum were present at all three; Corynoneura and Paratanytarsu at DC1 only; Cricotopus at DC1 and DC3; Apedilum elachistus notably at DC2 and DC3; and Parametriocnemus only at DC2. C. calligraphus individuals from DC1 showed no mentum deformities; only 2 from DC2 exhibited mouth-structure alterations; while specimens from DC3 presented the most abnormalities, especially during autumn and late winter. Type-II deformities (supernumerary teeth and gaps) were the most common. Anatomical deformities are sublethal effects representing an early alert to chemically caused environmental degradation. Mentum deformities in benthic-Chironomidae larvae

Ionizing radiation and taxonomic, functional and evolutionary diversity of bird communities.

PubMed

Morelli, Federico; Benedetti, Yanina; Mousseau, Timothy A; Møller, Anders Pape

2018-08-15

Ionizing radiation from nuclear accidents at Chernobyl, Fukushima and elsewhere has reduced the abundance, species richness and diversity of ecosystems. Here we analyzed the taxonomic, functional and evolutionary diversity of bird communities in forested areas around Chernobyl. Species richness decreased with increasing radiation, mainly in 2007. Functional richness, but not functional evenness and divergence, decreased with increasing level of ionizing radiation. Evolutionary distinctiveness of bird communities was higher in areas with higher levels of ionizing radiation. Regression tree models revealed that species richness was higher in bird communities in areas with radiation levels lower than 0.7 μSv/h. In contrast, when radiation levels were higher than 16.67 μSv/h, bird species richness reached a minimum. Functional richness was affected by two variables: Forest cover and radiation level. Higher functional richness was found in bird communities in areas with forest cover lower than 50%. In the areas with forest cover higher than 50%, the functional richness was lower when radiation level was higher than 0.91 μSv/h. Finally, the average evolutionary distinctiveness of bird communities was higher in areas with forest cover exceeding 50%. These findings imply that level of ionizing radiation interacted with forest cover to affect species richness and its component parts, i.e. taxonomic, functional, and evolutionary diversity. Copyright © 2018 Elsevier Ltd. All rights reserved.

A taxonomic review of the centipede genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) in mainland Southeast Asia, with description of a new species from Laos

PubMed Central

Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Tongkerd, Piyoros; Panha, Somsak

2016-01-01

Abstract The centipede genus Scolopendra in mainland Southeast Asia is reviewed taxonomically based on morphological characters, informed by a molecular phylogenetic analysis using sequences from three mitochondrial and nuclear genes (COI, 16S rRNA and 28S rRNA). Eight nominal species of Scolopendra, namely Scolopendra morsitans Linnaeus, 1758, Scolopendra subspinipes Leach, 1816, Scolopendra dehaani Brandt, 1840, Scolopendra multidens Newport, 1844, Scolopendra calcarata Porat, 1876, Scolopendra japonica Koch, 1878, Scolopendra pinguis Pocock, 1891, and Scolopendra dawydoffi Kronmüller, 2012, are redescribed together with some revision of type materials. Geographical variation in each species has been compiled with reference to samples that span their distribution ranges in Southeast Asia and some parts of neighbouring areas such as East Asia, the Indian Ocean, and Africa. Comparative study of traditional taxonomic characters from external morphology provides further information to distinguish some closely related species. Scolopendra cataracta Siriwut, Edgecombe & Panha, sp. n., is described from the southern part of Laos, with additional records in Thailand and Vietnam. The phylogenetic framework for Southeast Asian Scolopendra recognizes Scolopendra calcarata + Scolopendra pinguis, Scolopendra morsitans, and a Scolopendra subspinipes group that unites the other six species as the main clades. Within the Scolopendra subspinipes group, two monophyletic groups can be distinguished by having either slender or short, thick ultimate leg prefemora and different numbers of apical spines on the coxopleuron. Scolopendra arborea Lewis, 1982, is placed in subjective synonymy with Scolopendra dehaani. A survey of external morphology of the genital segments confirms its potential for improving species identification in Scolopendra. Some observations on biology and behaviour are recorded based on field surveys in this area. PMID:27408540

Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering.

PubMed

Gupta, Kushol; Contreras, Lydia M; Smith, Dorie; Qu, Guosheng; Huang, Tao; Spruce, Lynn A; Seeholzer, Steven H; Belfort, Marlene; Van Duyne, Gregory D

2014-04-01

The stable ribonucleoprotein (RNP) complex formed between the Lactococcus lactis group II intron and its self-encoded LtrA protein is essential for the intron's genetic mobility. In this study, we report the biochemical, compositional, hydrodynamic and structural properties of active group II intron RNP particles (+A) isolated from its native host using a novel purification scheme. We employed small-angle X-ray scattering to determine the structural properties of these particles as they exist in solution. Using sucrose as a contrasting agent, we derived a two-phase quaternary model of the protein-RNA complex. This approach revealed that the spatial properties of the complex are largely defined by the RNA component, with the protein dimer located near the center of mass. A transfer RNA fusion engineered into domain II of the intron provided a distinct landmark consistent with this interpretation. Comparison of the derived +A RNP shape with that of the previously reported precursor intron (ΔA) particle extends previous findings that the loosely packed precursor RNP undergoes a dramatic conformational change as it compacts into its active form. Our results provide insights into the quaternary arrangement of these RNP complexes in solution, an important step to understanding the transition of the group II intron from the precursor to a species fully active for DNA invasion.

Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera).

PubMed

Stelzer, Claus-Peter; Riss, Simone; Stadler, Peter

2011-04-07

Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels--within and among genealogical species--and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.