Sketched reference databases for genome-based taxonomy and comparative genomics / Bases de dados de referência esboçados para taxonomia baseada em genoma e genômica comparativa

The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor's exploration and selection, among others.

A análise de dados genômicos, metagenômicos e proteômicos com curadoria é de suma importância nos campos da biologia, medicina, educação e bioinformática. Embora esse tipo de dados geralmente seja hospedado em formato bruto em repositórios internacionais gratuitos, o acesso total requer muita capacidade de computação e grande espaço em disco de armazenamento para o usuário doméstico. Os objetivos do estudo são oferecer um conjunto abrangente de bancos de dados de referência genômica e proteômica microbiana de forma acessível e fácil de usar para a comunidade científica e demonstrar suas vantagens e utilidade. Além disso, apresentamos um estudo de caso sobre a aplicabilidade dos dados esboçados para a determinação da coerência genômica geral entre dois membros da família Brucellacea, o que sugere que eles pertencem às mesmas genomoespécies que permanecem como ecótipos discretos. Um conjunto representativo de genomas, proteomas (de material tipo) e metagenomas foi coletado diretamente do banco de dados NCBI Assembly e do banco de dados de taxonomia do genoma (GTDB), associada aos principais grupos de bactérias, Archaea, vírus e fungos. Bancos de dados esboçados foram subsequentemente criados e armazenados em representações reduzidas práticas usando o algoritmo MinHash implementado no software Mash. O conjunto de dados obtido contém mais de 133 GB de espaço em disco reduzido para 883,25 MB e representa 125,110 registros genômicos/proteômicos de oito contextos informativos, que foram pré-filtrados para torná-los acessíveis, utilizáveis ​​e amigáveis ​​com recursos computacionais limitados. Os usos potenciais desses bancos de dados esboçados são discutidos, incluindo, mas não se limitando, a delimitação de espécies microbianas, estimativa de distâncias genômicas e novidades genômicas, comparações emparelhadas entre proteomas, genomas e metagenomas, exploração e seleção filogenética de vizinhos, entre outros.

Lost and Found: Taxonomic Notes on Some Butterflies (Lepidoptera: Papilionoidea) from J.F. Zikán found on F. Dissmann's Collection.

J. F. Zikán described several new taxa of butterflies from the Neotropical region. The majority of the butterfly types of J. F. Zikán was deposited at the Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (IOC). However, some type series were found to be incomplete. The present paper discusses and illustrate some type specimens of Papilionidae and Nymphalidae from J. F. Zikán found in Dissmann's collection, that now is deposited at Museu de Diversidade Biológica from University of Campinas - UNICAMP, Campinas, São Paulo, Brazil (ZUEC).

An annotated catalogue of Echinodermata types in the Museu de Zoologia, Universidade de São Paulo, Brazil

The types of nominal species of Echinodermata in the collection of the Museu de Zoologia, Universidade de São Paulo are catalogued: Holothuroidea (19 species ­ 16 holotypes, 1 paratype and 2 neotypes) and Ophiuroidea (4 species ­ 1 neotype and 3 paratypes). Photographs of all the type specimens are given. A brief account of the history of the MZUSP's echinoderm collections is presented.(AU)

On the identities of Neotropical Stegana species (Diptera, Drosophilidae). III. Four Costa Rican species described by J. R. Malloch

ABSTRACT The identities of the following four New World species of Stegana from Costa Rica, Stegana atrimana Malloch, 1924, Stegana nigrita Malloch, 1924, Stegana schildi Malloch, 1924, and Stegana tempifera Malloch, 1924, are clarified, and their redescriptions are provided. According to the original descriptions, the holotypes of the four species, deposited in the National Museum of Natural History (USNM), were males. However, upon dissection of their terminalia, we realized that all but one (S. tempifera) are females. Therefore, redescriptions of their external morphology (and/or terminalia) are mainly based on male paratypes, except for S. schildi, which is based on a male non-type specimen from Panama bearing Malloch's handwritten identification label. Photomicrographs of the habitus and terminalia, in addition to china ink drawings of the aedeagi and associated sclerites, are included.

Contributions to the knowledge of Neotropical Lycaenidae: taxonomy of Johnsonita/ Salazar amp; Constantino, 1995 with descriptions of seven new species (Theclinae: Eumaeini).

The Transandean-Andean genus Johnsonita Salazar Constantino, 1995 is revised on the basis of wing and genitalia morphology. Apart from eight species formerly placed in Johnsonita (Thecla assula Draudt, 1919; Thecla auda Hewitson, 1867; Thecla catadupa Hewitson, 1869; Thecla chaluma Schaus, 1902, Thecla chlamydem Druce, 1907; Thecla pardoa d'Abrera, 1995; Johnsonita johnsoni Salazar Constantino, 1995 and Johnsonita johnbanksi Bálint, 2003), seven new species are described: Johnsonita carpia Bálint, Boyer Pyrcz, sp. n. (Ecuador), Johnsonita iacinta Bálint, Boyer Pyrcz, sp. n. (Peru), Johnsonita ianusca Bálint, Lorenc-Brudecka Pyrcz, sp. n. (Ecuador), Johnsonita oxalida Bálint, Boyer Pyrcz, sp. n. (Peru), Johnsonita subcunicula Bálint, Cerdeña Pyrcz, sp. n. (Peru), Johnsonita turquisca Bálint, Boyer Pyrcz, sp. n. (Ecuador) and Johnsonita zubkova Bálint, Boyer Lorenc-Brudecka, sp. n. (Peru). One species, erroneously recorded from Bolivia under the name Thecla chaluma Schaus, 1902, is not formally described due to insufficient material. An identification key, type material revision, descriptions or redescriptions, and diagnosis for all the taxa recognized are given. Lectotypes for the nominal species Thecla assula Draudt, 1919 and Thecla chlamydem Druce, 1907 are designated. Male secondary wing characters are tabulated. A brief discussion on classification, life-history and male secondary characters of Johnsonita is presented.

An illustrated catalogue of the types of Blephariceridae (Diptera) in the collection of Museu de Zoologia da Universidade de São Paulo, Brazil

Kelloggina Williston, 1907 is one of the least studied Blephariceridae genera in the world, despite being the most diverse in the Neotropics with 34 species. We provide a catalogue with the 14 nominal species of the genus described by Lane and dAndretta from the Southeastern Region of Brazil, of which the type-specimens are deposited at the Diptera Collection of the Museu de Zoologia da Universidade de São Paulo. There are 60 specimens deposited at this museum, including male holotypes of 14 species and females “allotypes” (paratypes) for seven species. We include male diagnoses and photographs of the holotypes of all species.(AU)

An illustrated catalogue of the types of Blephariceridae (Diptera) in the collection of Museu de Zoologia da Universidade de São Paulo, Brazil

Abstract KellogginaWilliston, 1907 is one of the least studied Blephariceridae genera in the world, despite being the most diverse in the Neotropics with 34 species. We provide a catalogue with the 14 nominal species of the genus described by Lane and dAndretta from the Southeastern Region of Brazil, of which the type-specimens are deposited at the Diptera Collection of the Museu de Zoologia da Universidade de São Paulo. There are 60 specimens deposited at this museum, including male holotypes of 14 species and females allotypes (paratypes) for seven species. We include male diagnoses and photographs of the holotypes of all species.

An illustrated catalogue of the types of Blephariceridae (Diptera) in the collection of Museu de Zoologia da Universidade de São Paulo, Brazil

Abstract KellogginaWilliston, 1907 is one of the least studied Blephariceridae genera in the world, despite being the most diverse in the Neotropics with 34 species. We provide a catalogue with the 14 nominal species of the genus described by Lane and d'Andretta from the Southeastern Region of Brazil, of which the type-specimens are deposited at the Diptera Collection of the Museu de Zoologia da Universidade de São Paulo. There are 60 specimens deposited at this museum, including male holotypes of 14 species and females "allotypes" (paratypes) for seven species. We include male diagnoses and photographs of the holotypes of all species.

Cataloguing Prof. Eudóxia M. Froehlich's wet collection of land planarians (Platyhelminthes, Geoplanidae): a bounty of type specimens of 78 species.

Zoologist Prof. Eudóxia Maria Froehlich (1929*-2015†) kept an uncatalogued personal collection of land planarians in wet medium. We catalogued their contents. Glass jars contained a variable number of small vials, each with one or several labeled specimens. We transcribed the species names and field data, when available, written on card labels to a table. A total of 1772 vials in 80 jars, contained over 2700 specimens. Subsequently, we cross checked field data with that of the type specimens. As a result, we identified, with different degrees of certainty, type specimens of 78 species. These types compose a very significant potential source of additional morphological details of the species to conform with current standards in the taxonomy of the group.

Type specimens of true bugs (Hemiptera: Heteroptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil

This paper provides a record of the type specimens of Heteroptera (Insecta: Hemiptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil (MZUSP), with information on 65 primary types and 316 secondary types. These type specimens represent 116 nominal species, currently classified in five infraorders and 14 families. The taxa are presented alphabetically, followed by bibliographic citation, type status, preservation method, collection data, and taxonomic remarks when appropriate.(AU)

Catalogue of type specimens of Insecta (Arthropoda: Hexapoda) deposited in the entomological collection of the Museum of Zoology of Universidade Estadual de Feira de Santana, Brazil.

This contribution is an update catalogue of the type specimens of Insecta deposited in the entomological collection Prof. Johann Becker of the Museum of Zoology of Universidade Estadual de Feira de Santana, Bahia, Brazil. A list of 206 holtypes and 1,430 paratypes of 23 families, 73 genera, and 244 species allocated in 12 orders. Lectotype and paralectotypes of Bitoma palmarum Bondar, 1940 were designated. Diptera present the highest number of types on the collection, with 161 holotypes and 1,324 paratypes.

Catalogue of Rangomaramidae (Diptera: Bibionomorpha) types housed in the collection of the Museu de Zoologia da Universidade de São Paulo, Brazil

This paper provides a catalogue of the type specimens of Rangomaramidae (Diptera: Bibionomorpha) held in the collection of the Museu de Zoologia da Universidade de São Paulo, Brazil (MZUSP). Label data and the condition of 26 type-specimens (three holotypes and 23 paratypes) of four Neotropical species are provided.(AU)

Catalogue of Rangomaramidae (Diptera: Bibionomorpha) types housed in the collection of the Museu de Zoologia da Universidade de São Paulo, Brazil

This paper provides a catalogue of the type specimens of Rangomaramidae (Diptera: Bibionomorpha) held in the collection of the Museu de Zoologia da Universidade de São Paulo, Brazil (MZUSP). Label data and the condition of 26 type-specimens (three holotypes and 23 paratypes) of four Neotropical species are provided.

Type specimens of true bugs (Hemiptera: Heteroptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil

This paper provides a record of the type specimens of Heteroptera (Insecta: Hemiptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil (MZUSP), with information on 65 primary types and 316 secondary types. These type specimens represent 116 nominal species, currently classified in five infraorders and 14 families. The taxa are presented alphabetically, followed by bibliographic citation, type status, preservation method, collection data, and taxonomic remarks when appropriate.

Type specimens of true bugs (Hemiptera: Heteroptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil

Abstract This paper provides a record of the type specimens of Heteroptera (Insecta: Hemiptera) housed in the Museu de Zoologia da Universidade de São Paulo, Brazil (MZUSP), with information on 65 primary types and 316 secondary types. These type specimens represent 116 nominal species, currently classified in five infraorders and 14 families. The taxa are presented alphabetically, followed by bibliographic citation, type status, preservation method, collection data, and taxonomic remarks when appropriate.

Catalogue of Psocoptera (Insecta: Psocodea) types housed in the collection of the Museu de Zoologia da Universidade de São Paulo

A catalogue of type specimens of Psocoptera (Insecta: Psocodea) deposited in the collection of the Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil, is presented and updated to February, 2019. 45 holotypes and 47 paratypes of 52 species were found, included in the suborders Psocomorpha and Trogiomorpha, and listed in the families Amphipsocidae, Asiopsocidae, Caeciliusidae (infraorder Caeciliusetae); Lachesillidae and Pseudocaeciliidae (infraorder Homilopsocidea); Philotarsidae (infraorder Philotarsetaea) Hemipsocidae, Myopsocidae and Psocidae (infraorder Psocetae); Ptiloneuridae (infraorder Epipsocetae), and Lepidopsocidae (infraorder Atropetae). The taxa are presented alphabetically by suborders, infraorders, families, subfamilies, tribes and genera, followed by species (updated to the valid name), bibliographic citation, type category, description of the type condition with collection number and method of preservation. When necessary, comments are added.(AU)

Catalogue of Psocoptera (Insecta: Psocodea) types housed in the collection of the Museu de Zoologia da Universidade de São Paulo

A catalogue of type specimens of Psocoptera (Insecta: Psocodea) deposited in the collection of the Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil, is presented and updated to February, 2019. 45 holotypes and 47 paratypes of 52 species were found, included in the suborders Psocomorpha and Trogiomorpha, and listed in the families Amphipsocidae, Asiopsocidae, Caeciliusidae (infraorder Caeciliusetae); Lachesillidae and Pseudocaeciliidae (infraorder Homilopsocidea); Philotarsidae (infraorder Philotarsetaea) Hemipsocidae, Myopsocidae and Psocidae (infraorder Psocetae); Ptiloneuridae (infraorder Epipsocetae), and Lepidopsocidae (infraorder Atropetae). The taxa are presented alphabetically by suborders, infraorders, families, subfamilies, tribes and genera, followed by species (updated to the valid name), bibliographic citation, type category, description of the type condition with collection number and method of preservation. When necessary, comments are added.

Taxonomic revision of four species of the Neotropical land planarian genera Cratera and Geoplana (Platyhelminthes, Tricladida) with a description of two new species and an emendation of Cratera.

The Brazilian land planarians Cratera crioula, C. joia, Geoplana hina, and G. taxiarcha (Platyhelminthes, Tricladida, Geoplanidae) are revised taxonomically from type material and additional specimens. Geoplana hina sensu Carbayo et al. (2013) was found to be an undescribed species and therefore is described and named as Cratera picuia sp. n. A new species of the genus is also described and named as Cratera arucuia sp. n. G. hina and G. taxiarcha are transferred to Cratera. The most remarkable morphological feature of Cratera-a dilated terminal portion of the ejaculatory duct-is either absent, inconspicuous, or variable in C. hina, C. joia, C. picuia sp. n., and C. arucuia sp. n. Based on the monophyletic status of Cratera inferred elsewhere, an emendation of the genus is here proposed to encompass the morphological variation observed in the genus.

New synonymies, new combinations and lectotype designations for weevils in the tribe Naupactini (Coleoptera: Curculionidae: Entiminae).

We examined the type material of 15 species of Naupactus Dejean and related genera (Curculionidae: Entiminae), most of them described by Alphonse Hustache (Museum National d'Histoire Naturelle, Paris) and Carl Boheman (Naturhistoriska Riksmuseet, Stockholm). The information associated with the types was compared with the original descriptions, and large series of specimens were examined in order to analyze the variation of each species throughout its range (sexual dimorphism, other kinds of polymorphism or geographic variation). Based on the results of this study we establish seven new combinations, one new placement and nine new synonymies, we make 21 lectotype designations and provide three new country and state records. Alceis curtus (Boh.), Lanterius leucophaeus (Boh.), L. sparsus (Boh.), L. sellatus (Boh.), Parapantomorus carinirostris (Hust.), Symmathetes signatus (Blanchard) and Teratopactus acerbus (Boh.) are new combinations and T. sulphureoviridis Hust. is a new placement. The following names are senior synonyms of those between parentheses: Lanterius inermis (Hust.) (syn. Macrostylus ocellatus Lanteri); Naupactus auricinctus Boh. (syn. N. ruficornis Boh.); N. bridgesii G.R. Waterhouse (syn. N. angulithorax Hust.); N. condecoratus Boh. (syn. N. bosqi Hust.); N. cyphoides (Heller) (syn. N. calamuchitanensis Hust., N. viridinitens Hust, N. viridulus Hust.); N. peregrinus (Buchanan) (syn. N. brevicrinitus Hust.); and Trichonaupactus densior Hust. (syn. T. rexus Hust.). For each species we provide the following information: synonyms, available data on type specimens (sex, body length, geographic location, kind of type, and repository), complete geographic distribution, pictures of types or specimens compared with types, an explanation about the reasons that justify the nomenclatural acts.

Catalogue of Neotropical Curtonotidae (Diptera, Ephydroidea)

The Neotropical species of Curtonotidae are updated and catalogued. A total of 33 species names are listed, including two fossil taxa and one nomem dubium. Valid and invalid names and synonyms are presented, totaling 45 names. Bibliographic references are given to all listed species, including information about name, author, year of publication, page number, type species and type locality. Lectotype and paralectotypes are designated to Curtonotum punctithorax (Fischer, 1933). Curtonotum simplex Schiner, 1868 stat. rev. is recognized as a valid name.(AU)