scholarly journals New records of the bats Histiotus montanus and Molossops neglectus in southeastern Brazil with notes on biology and morphology

Caldasia ◽  
2020 ◽  
Vol 42 (1) ◽  
pp. 30-37
Author(s):  
Renato Gregorin ◽  
Matheus C. S. Mancini ◽  
Rafael S. Laurindo ◽  
Rodrigo Mello ◽  
Ligiane M. Moras ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
South America ◽  
Morphological Variation ◽  
Rare Species ◽  
New Records ◽  
Principal Component ◽  
Biological Data ◽  
Southeastern Brazil ◽  
Morphometric Variation ◽  
Aerial Insectivore

Distributional and biological data for some bat species in South America are scarce, mainly in non-phyllostomid bats. Herein we provide new records of two rare species of aerial insectivore bats for southeastern Brazil, Histiotus montanus and Molossops neglectus. In addition, we report facial morphological variation in color and new records of ectoparasites for H. montanus. For M. neglectus we performed a Principal Component Analysis (PCA) to check for morphometric variation based on forearm and skull dimensions, the southerly distributed specimens showing slightly smaller measurements than the northern ones.

Distribution of the dwarf dog-faced bat Molossops temminckii (Chiroptera: Molossidae) in Colombia and comments on its morphometry

Mammalia ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Julio J. Chacón-Pacheco ◽  
Luis José Avendaño Maldonado ◽  
Carlos Agamez-López ◽  
Ingrith Yuliany Mejía-Fontecha ◽  
Daniela Velásquez-Guarín ◽  
...  
Keyword(s):  
South America ◽  
Morphological Variation ◽  
Principal Component ◽  
The Other ◽  
Cryptic Diversity ◽  
Vocal Plasticity ◽  
Morphometric Variation ◽  
Integrative Analyses ◽  
Principal Component Analyses

AbstractThe genus Molossops includes two species that are restricted to South America: Molossops neglectus and Molossops temminckii. The smaller dog-faced dwarf Molossops temminckii is distributed from Colombia to Argentina and has a wide morphological variation and vocal plasticity. In Colombia, this species remains poorly known. To fill distributional gaps, we present novel records from Arauca, Atlántico, Bolívar, Córdoba, and Huila departments. We also present an analysis of the morphometric variation in South America using Principal Component Analyses. These show an external and cranial difference of specimens of Colombia in respect of other and South America populations. In Colombian landscapes dominated by the floodplain savanna of the Orinoco region, Molossops temminckii is smaller than in the other regions of the country, and the previously suggested existence of cryptic diversity within the taxon should be evaluated. Therefore, we suggest further integrative analyses to investigate a possible subspecific status of some Colombian populations.

Morphological variation in the genus Juliomys (Rodentia: Cricetidae: Sigmodontinae) and taxonomic status of Juliomys anoblepas (Winge 1887) from the Quaternary of Southeast Brazil

Zootaxa ◽  
2020 ◽  
Vol 4861 (3) ◽  
pp. 429-443
Author(s):  
CAROLINA PIRES ◽  
MARCELO WEKSLER ◽  
CIBELE R. BONVICINO
Keyword(s):  
Principal Component Analysis ◽  
Morphological Variation ◽  
Morphological Analysis ◽  
Principal Component ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
The Other ◽  
Anterior Portion ◽  
Living Species ◽  
Qualitative Characters

The region of Lagoa Santa, Minas Gerais, Brazil, is one of the most important karstic areas of the Brazilian Quaternary due to the faunistic diversity of living and extinct forms. Among them, some taxa remain poorly studied, as is the case of Calomys anoblepas Winge 1887. Despite the recent allocation of the taxon within Juliomys, its description and morphological analysis are condensed, based on comparative few specimens and on few informative characters. In this study, we investigate characters proposed to distinguish species of Juliomys, and reevaluate the taxonomic status of the fossil Juliomys anoblepas. We analyzed 80 cranio-dental morphological characters in 233 specimens represented by the four species currently recognized: J. pictipes (Osgood 1933), J. rimofrons Oliveira & Bonvicino 2002, J. ossitenuis Costa, Pavan, Leite & Fagundes 2007, and J. ximenezi Christoff, Vieira, Oliveira, Gonçalves, Valiati & Tomasi 2016. We also performed principal component analysis on eight craniodental measurements available for the J. anoblepas hypodigm. The review of morphological systems and the evaluation of the characters used in the literature revealed that there are no diagnostic characters in the anterior portion of the skull and in the molar series of Juliomys, being difficult to differentiate the fossil from the other living species. Only six qualitative characters were variable and applicable to the hypodigm of J. anoblepas. Characters are polymorphic, invariable, or the fossil is not sufficiently complete to determinate its states. The taxon could not be morphometrically differentiated from J. pictipes and J. ossitenuis. Based on the results presented herein, we consider J. anoblepas as a nomen dubium and restrict its name to the taxon’s hypodigm. 

scholarly journals Morphological and molecular identification of hairtail (Trichiurus spp.) caught in Pangandaran Waters

2020 ◽  
Vol 147 ◽  
pp. 02021
Author(s):  
Tia Aprianti Lestari ◽  
Murwantoko Murwantoko ◽  
Eko Setyobudi
Keyword(s):  
Principal Component Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Principal Component ◽  
Component Analysis ◽  
Rrna Gene ◽  
Morphometric Variation ◽  
Dorsal Fin ◽  
Fish Samples

This study aimed to identify the species of hairtail caught in Pengandaran waters based on morphological, meristic character and molecular approach. In total 135 fish samples were collected from Pangandaran Waters, during March-April 2017. Each sample was identified, measured on 22 morphometric and 4 meristic characters, then analyzed using Principal Component Analysis (PCA). Molecular identification was conducted by sequenced of 16S rRNA gene. The result of the research showed that hairtail characterized by III spines and 125-140 soft rays of dorsal fin (D.III, 125-140), the anal fin situated below 38th to 41th of dorsal-fin soft ray, I spine and 10 soft rays of pectoral fin (P.I.10), and I spine and 91 to 112 spinules of anal fin (A.I.91-112). Based on the morphological identification, the hairtail was belonged to Trichiurus lepturus. Principal Component Analysis showing the morphometric variation was presented in the caudal peduncle length. Molecular analysis of mitochondrial DNA of the partial 16S rRNA gene confirmed the hairtail as T. lepturus with similarity 98-99% based on previously published data. Phylogenetic analysis showed that T. lepturus from Pangandaran were closely similar to related species caught from the Southern Coast of Yogyakarta Special Territory (Indian Ocean) and Hainan China (Pacific Ocean).

Morphological variation in the Pacific sand dollar Dendraster excentricus

1995 ◽  
Vol 73 (3) ◽  
pp. 576-583
Author(s):  
Raymond K. Nakamura
Keyword(s):  
Principal Component Analysis ◽  
Principal Components ◽  
Morphological Variation ◽  
Correlation Matrix ◽  
Principal Component ◽  
Sand Dollar ◽  
Coastal Habitats ◽  
Point Conception ◽  
The Pacific ◽  
Dendraster Excentricus

Correlations between latitude, habitat, and morphology in the Pacific sand dollar Dendraster excentricus were identified with principal component analysis. Twenty-two lengths were measured on the oral and aboral surfaces of 615 specimens from 31 sites. Samples were divided at latitude 34°30′N (Point Conception) and into bay and coastal habitats by relative wave exposure. Principal components (PC) were estimated from a correlation matrix of sample means of log-transformed measurements. PC1 accounted for 90% of the variance and was a measure of overall size. All 22 PC1 coefficients were positive and differed significantly from 0, according to a jackknifing test. PC1 differed significantly with latitude (ANOVA, p < 0.01) but not habitat. Southern populations tended to be smaller. PC2 accounted for 5% of the variance and described overall shape. Of the 22 variables, 13 had significant coefficients that varied in sign. PC2 varied significantly with habitat (ANOVA, p < 0.05) but not latitude. In coastal populations, the peristome and petaloids tended to be more posteriorly positioned and the food grooves were branched more peripherally. These features correspond to the greater tendency for coastal specimens to use their posterior end to suspension feed.

scholarly journals New records of Ichneumonidae (Hymenoptera: Ichneumonoidea) from a coffee agroecosystem of southeastern Brazil

2020 ◽  
Vol 2 ◽  
pp. ec02031
Author(s):  
Daniell R. R. Fernandes ◽  
Rogéria I. R. Lara ◽  
Nelson W. Perioto
Keyword(s):  
South America ◽  
New Records ◽  
Sao Paulo ◽  
The State ◽  
Southeastern Brazil ◽  
Nominal Species ◽  
São Paulo ◽  
First Time

We analyzed 614 specimens of Ichneumonidae (Hymenoptera: Ichneumonoidea) collected from a coffee agro-ecosystem located at Cravinhos, São Paulo, Brazil, and 34 nominal species were identified belonging to 22 genera and 10 subfamilies. Temelucha hilux Gauld, 2000 and Xiphosomella bonera Gauld, 2000 were recorded for the first time in South America, Colpotrochia diabella Gauld & Sithole, 2002 for the first time in Brazil, and Acerastes pertinax (Cresson, 1872), Colpotrochia mexicana (Cresson, 1868), Colpotrochia neblina Gauld & Sithole, 2002, Colpotrochia texana (Cresson, 1872), Diplazon mulleolus Dasch, 1964, Eiphosoma nigrovittatum Cresson, 1865, Enicospilus flavus (Fabricius, 1775), Enicospilus glabratus (Say, 1835), Enicospilus purgatus (Say, 1835), Lymeon haemorrhoidalis (Taschenberg, 1876), Mesostenus alvarengae Porter, 1973, Microcharops plaumanni Gupta, 1987, Nonnus niger (Brullé, 1846), Ophiogastrella maculithorax Brues, 1912, Pachysomoides stupidus (Cresson, 1874), Polycyrtus albolineatus Cameron, 1911, and Trieces horisme Gauld & Sithole, 2002 for the first time in the state of São Paulo. Other 14 species had been already registered for the state of São Paulo, and for the first time, were being recorded in relation to a coffee agro-ecosystem.

scholarly journals Exploring High-Dimensional Biological Data with Sparse Contrastive Principal Component Analysis

2019 ◽  
Author(s):  
Philippe Boileau ◽  
Nima S. Hejazi ◽  
Sandrine Dudoit
Keyword(s):  
Principal Component Analysis ◽  
Dimensionality Reduction ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Component Analysis ◽  
Biological Data ◽  
Sequencing Data ◽  
Microarray Gene Expression ◽  
Biological Signal ◽  
Reduction Techniques

AbstractMotivationStatistical analyses of high-throughput sequencing data have re-shaped the biological sciences. In spite of myriad advances, recovering interpretable biological signal from data corrupted by technical noise remains a prevalent open problem. Several classes of procedures, among them classical dimensionality reduction techniques and others incorporating subject-matter knowledge, have provided effective advances; however, no procedure currently satisfies the dual objectives of recovering stable and relevant features simultaneously.ResultsInspired by recent proposals for making use of control data in the removal of unwanted variation, we propose a variant of principal component analysis, sparse contrastive principal component analysis, that extracts sparse, stable, interpretable, and relevant biological signal. The new methodology is compared to competing dimensionality reduction approaches through a simulation study as well as via analyses of several publicly available protein expression, microarray gene expression, and single-cell transcriptome sequencing datasets.AvailabilityA free and open-source software implementation of the methodology, the scPCA R package, is made available via the Bioconductor Project. Code for all analyses presented in the paper is also available via GitHub.

scholarly journals IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rong Zhu ◽  
Yong Wang ◽  
Jin-Xing Liu ◽  
Ling-Yun Dai
Keyword(s):  
Principal Component Analysis ◽  
Random Forest ◽  
Cross Validation ◽  
Search Algorithm ◽  
Principal Component ◽  
Component Analysis ◽  
Biological Data ◽  
Learning Technology ◽  
Disease Associations ◽  
Fold Cross Validation

Abstract Background Identifying lncRNA-disease associations not only helps to better comprehend the underlying mechanisms of various human diseases at the lncRNA level but also speeds up the identification of potential biomarkers for disease diagnoses, treatments, prognoses, and drug response predictions. However, as the amount of archived biological data continues to grow, it has become increasingly difficult to detect potential human lncRNA-disease associations from these enormous biological datasets using traditional biological experimental methods. Consequently, developing new and effective computational methods to predict potential human lncRNA diseases is essential. Results Using a combination of incremental principal component analysis (IPCA) and random forest (RF) algorithms and by integrating multiple similarity matrices, we propose a new algorithm (IPCARF) based on integrated machine learning technology for predicting lncRNA-disease associations. First, we used two different models to compute a semantic similarity matrix of diseases from a directed acyclic graph of diseases. Second, a characteristic vector for each lncRNA-disease pair is obtained by integrating disease similarity, lncRNA similarity, and Gaussian nuclear similarity. Then, the best feature subspace is obtained by applying IPCA to decrease the dimension of the original feature set. Finally, we train an RF model to predict potential lncRNA-disease associations. The experimental results show that the IPCARF algorithm effectively improves the AUC metric when predicting potential lncRNA-disease associations. Before the parameter optimization procedure, the AUC value predicted by the IPCARF algorithm under 10-fold cross-validation reached 0.8529; after selecting the optimal parameters using the grid search algorithm, the predicted AUC of the IPCARF algorithm reached 0.8611. Conclusions We compared IPCARF with the existing LRLSLDA, LRLSLDA-LNCSIM, TPGLDA, NPCMF, and ncPred prediction methods, which have shown excellent performance in predicting lncRNA-disease associations. The compared results of 10-fold cross-validation procedures show that the predictions of the IPCARF method are better than those of the other compared methods.

Taxonomic revision of the Colombian Tityus (Archaeotityus) (Scorpiones, Buthidae) species: a morphological and morphometric approach, with a description of a new species

Zootaxa ◽  
2019 ◽  
Vol 4660 (1) ◽  
pp. 1-94
Author(s):  
JAIRO A. MORENO-GONZÁLEZ ◽  
RANULFO GONZÁLEZ O. ◽  
EDUARDO FLÓREZ D.
Keyword(s):  
Principal Component Analysis ◽  
New Species ◽  
New Records ◽  
Principal Component ◽  
Taxonomic Revision ◽  
Component Analysis ◽  
Morphological Characters ◽  
Species Level ◽  
Qualitative And Quantitative ◽  
A New Species

We present a taxonomic revision of the Colombian Tityus (Archaeotityus) species based on morphological and morphometric evidence. We examined more than 385 specimens and evaluated new and previously used qualitative and quantitative morphological characters. We redescribe the Colombian species and present morphological characters for both sexes and an emended diagnosis for the subgenus Tityus (Archaeotityus). We describe a new species Tityus guane sp. nov. from Santander department, Colombia, Tityus betschi Lourenço 1992 is synonymized with Tityus parvulus Kraepelin, 1914, and Tityus wayuu Rojas-Runjaic & Armas, 2007 is synonymized with Tityus tayrona Lourenço, 1991. We measured 186 specimens and performed a multivariate principal component analysis (PCA) for 34 selected morphometric ratios for each sex. We found that a few morphological ratios support species level distinctions within the Colombian species. We provide updated distributional maps with new records and an identification key for both sexes. Furthermore, we provide an updated checklist for the subgenus and a discussion about the character systems used within Tityus (Archaeotityus). The new morphological characters proposed and the traditional morphometry examined with a PCA are useful for studying Tityus (Archaeotityus) taxonomy.

An assessment of morphometric and molecular variation in Monodelphis dimidiata (Wagner, 1847) (Didelphimorphia: Didelphidae)

Zootaxa ◽  
2010 ◽  
Vol 2646 (1) ◽  
pp. 26 ◽  
Author(s):  
JÚLIO FERNANDO VILELA ◽  
CLAUDIA AUGUSTA DE MORAES RUSSO ◽  
JOÃO ALVES DE OLIVEIRA
Keyword(s):  
Principal Component ◽  
Taxonomic Status ◽  
Genetic Distances ◽  
Canonical Variate ◽  
Southeastern Brazil ◽  
Bootstrap Support ◽  
Buenos Aires Province ◽  
Morphometric Data ◽  
Multivariate Statistical ◽  
Morphometric Variation

This study aims to clarify the taxonomic status of Monodelphis dimidiata and M. sorex, using molecular and morphometric data. Cytochrome-b sequences were obtained from specimens morphologically assignable to those taxa from the vicinity of type localities, but also representing their presumptive area of sympatry and extremes in their known distributions. These sequences were compared to GenBank downloaded sequences of select Monodelphis spp. and also of Marmosa lepida, Micoureus demerarae, and Didelphis albiventris, used as outgroups. Genetic distances and maximum likelihood analyses were performed to recover phylogenetic affinities among taxa. To access morphometric variation, univariate and multivariate statistical methods (Principal Component Analysis and Canonical Variate Analysis) were applied to the covariance matrix of 25 craniometric measurements obtained from a total of 108 specimens sampled across the geographic ranges of the species. The molecular analyses revealed a clade composed by haplotypes assignable to Monodelphis dimidiata and M. sorex (sensu Pine and Handley 2007) as distinct from the remaining Monodelphis species sampled to date, with 100% bootstrap support. Within this clade, one haplotype from Itatiaia was the sister clade to the remaining 11 specimens from Montevideo (Uruguay), Rio Grande do Sul and Santa Catarina states (Brazil), which formed an assemblage without clear geographic arrangement. In the morphometric analyses, the first two principal components of morphometric data separated variables associated with general latent size comparably expressed in all samples, and a group of variables including molars widths, molar toothrow length, and postorbital constriction breadth, which separates the geographic samples in a sequence coincident, to a large extent, with their latitudinal distributions. The sample from Itatiaia, Rio de Janeiro State, was again revealed as clearly distinct from the remaining samples, suggesting that it may represent a peripheral isolated population. With the study of original descriptions and published information on the type material of M. sorex, including photographs of syntypes, our analyses point to the recognition of M. sorex as a subjective junior synonym of M. dimidiata, which is then regarded as a widespread taxon ranging from the latitudes of southern Buenos Aires Province and Córdoba in Argentina to at least Minas Gerais State in southeastern Brazil, through the Pampas and the Atlantic Forest domains.

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