scholarly journals Distinguishing and employing sister species of fish in assessment of stream quality

2021 ◽  
Author(s):  
Fred Van Dyke ◽  
Benjamin W. van Ee ◽  
Seth Harju ◽  
Joshua W. Budi ◽  
Thomas B. Sokolowski ◽  
...  
Keyword(s):  
Habitat Quality ◽  
Dna Barcode ◽  
Sister Species ◽  
Individual Species ◽  
National Forests ◽  
Correct Identification ◽  
Similar Species ◽  
Slimy Sculpin ◽  
Mottled Sculpin ◽  
Stream Quality

Biological indicators (bioindicators) can be individual species or species groups used to assess habitat quality. Unfortunately, conservationists often lack information on species distribution, how to differentiate between similar species, and environmental conditions associated with the presence of a species. We addressed these problems using two “sister” species of fish, the Mottled Sculpin (Cottus bairdii) and the Slimy Sculpin (Cottus cognatus), as stream quality indicators in the Manistee River watershed in the Huron-Manistee National Forests in Michigan, USA. We determined the abundance and distribution of these species and related their presence to concurrent in-stream measurements of temperature, dissolved oxygen, pH, conductivity, turbidity, and stream quality score based on macroinvertebrate diversity. To be certain of identification, we sequenced the Cytochrome c Oxidase Subunit I (CO1) molecular marker for specimens and used it as a DNA barcode to determine a specimen’s species. Cladistic analyses of CO1 unambiguously supported recognition of Mottled Sculpin and Slimy Sculpin as distinct species, confirming initial 87.5% correct identification using morphological characteristics, with uncertainty limited to juvenile fish. Field determinations increased to 100% correct identification as investigators gained more experience. Both species were most abundant in headwater regions, decreased downstream, and were sympatric at several locations. Mottled Sculpin were more likely to be found at stream locations with lower conductivity, pH, and stream quality scores, whereas Slimy Sculpin presence was more strongly associated higher levels of DO and lower levels of turbidity. Such findings are important because Mottled Sculpin are a designated management indicator species of the US Forest Service in the Huron-Manistee National Forests, but may be ineffective as a habitat quality indicator when used alone. Concurrent use of Mottled Sculpin and Slimy Sculpin as a management indicator sister-species complex could allow sufficient landscape coverage to permit habitat assessment if species-specific differences in environmental tolerances are precisely determined.

scholarly journals Authentication of Chinese Crude Drug Gecko by DNA Barcoding

2011 ◽  
Vol 6 (1) ◽  
pp. 1934578X1100600 ◽  
Author(s):  
Hai-Feng Gu ◽  
Yun Xia ◽  
Rui Peng ◽  
Bang-Hui Mo ◽  
Li Li ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Habitat Destruction ◽  
Full Length ◽  
Correct Identification ◽  
Molecular Method ◽  
Specific Sequence ◽  
Gekko Gecko ◽  
Crude Drug

Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.

scholarly journals DNA Barcoding of Mosquitoes from the Pantanos de Centla Biosphere Reserve, Southeastern Mexico

2021 ◽  
Vol 37 (4) ◽  
pp. 198-207
Author(s):  
Aldo I. Ortega-Morales ◽  
Luis M. Hernández-Triana ◽  
Rahuel J. Chan-Chable ◽  
Javier A. Garza-Hernández ◽  
Vicente H. González-Álvarez ◽  
...  
Keyword(s):  
Mosquito Control ◽  
Mosquito Species ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Biosphere Reserve ◽  
Similar Species ◽  
Accurate Identification ◽  
Molecular Approaches ◽  
Species Complexes ◽  
Large Numbers

ABSTRACT Accurate identification of mosquito species is essential to support programs that involve the study of distribution and mosquito control. Numerous mosquito species are difficult to identify based only on morphological characteristics, due to the morphological similarities in different life stages and large numbers of some species that are members of morphologically similar species complexes. In the present study, the mosquitoes collected in the Pantanos de Centla Biosphere Reserve, southeastern Mexico, were evaluated using a combination of morphological and molecular approaches (mitochondrial cytochrome c oxidase subunit I [COI] DNA barcode). A total of 1,576 specimens of 10 genera and 35 species, mostly adult stages, were collected. A total of 225 COI DNA barcode sequences were analyzed; most species formed well-supported groups in the neighbor joining, maximum likelihood, and Bayesian inference trees. The intraspecific Kimura 2-parameter (K2P) genetic distance averaged 1.52%. An intraspecific K2P distance of 6.20% was observed in Anopheles crucians s.l., while a deep split was identified in Culex erraticus and Cx. conspirator. This study showed that COI DNA barcodes offer a reliable approach to support mosquito species identification in Mexico.

scholarly journals Impact of Urbanization to an Island and the Continent: Species Turnover and Nestedness in Neotropical Bird Assemblages

2021 ◽  
Vol 9 ◽  
Author(s):  
Sabina A. Caula ◽  
Virginia Sanz D'Angelo
Keyword(s):  
Negative Impact ◽  
Species Turnover ◽  
Bird Species ◽  
Urban Environments ◽  
Individual Species ◽  
Similar Species ◽  
Urban Gradient ◽  
Building Density ◽  
Urbanized Areas ◽  
Urban Matrix

Islands are well-known as particular and vulnerable ecosystems with evolutionary histories, environmental characteristics, and original communities different from those of continents. On the contrary, urban environments are recent, artificial, and structurally similar among distant regions. To assess the relative importance of regional and local processes on urban biota, we chose two urban environments, i.e., one on the mainland and another on an island in the same ecoregion. We asked whether the urbanization process affects the avian biodiversity of the ISLAND in the same way as in the continent. We defined an urban gradient with three levels of building density, namely, patches of native vegetation (remnant woodlands in the urban matrix), medium density urbanized areas that maintain vegetation along the streets and gardens, and residential areas with less vegetation cover and higher building density. In each geographical locality, we selected three sites (replicates) for each level of the urban gradient and did bird surveys. We found two times as many species in the urban landscape of the continent (69) as on the island (35), with the analogous richness decrease along the gradient in both regions. Species similarity was higher between urbanized sites of both regions compared with the similarity between woodlands and urbanized sites, showing that urban matrix filters similar species of each pool regionally. Individual species responded to urban structure in different ways. We found 32% of bird species were urban exploiters, 48% urban tolerant, and 20% urban avoiders in both regions. However, some species showed different frequencies of occurrence on the island and the continent. Species turnover contributed more than richness differences to species dissimilarity along the urban gradient on the continent. Contrarily, the nestedness component (i.e., species being a strict subset of the species at a richer site) was higher on the island. We concluded that the negative impact of highly urbanized areas on birds was stronger on the island than on the continent. Our results may help to assess the implications of beta-diversity loss, especially on islands.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Genome ◽  
2021 ◽  
Author(s):  
Leonardo Tresoldi Gonçalves ◽  
Filipe Michels Bianchi ◽  
Maríndia Deprá ◽  
Cláudia Calegaro-Marques
Keyword(s):  
Species Richness ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Fundamental Problem ◽  
Dna Barcode ◽  
Integrative Taxonomy ◽  
Correct Identification ◽  
Ecological Relevance ◽  
Definition Of ◽  
Barcode Gap

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5,241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

Two new and two poorly known autolytines (Polychaeta: Syllidae) from Madeira and the Mediterranean Sea

Zootaxa ◽  
2010 ◽  
Vol 2640 (1) ◽  
pp. 35 ◽  
Author(s):  
ARNE NYGREN ◽  
TOBIAS SUNDKVIST ◽  
BARBARA MIKAC ◽  
FREDRIK PLEIJEL
Keyword(s):  
New Species ◽  
Mediterranean Sea ◽  
New Genus ◽  
Molecular Data ◽  
Sister Species ◽  
White Spot ◽  
Similar Species ◽  
Mitochondrial Coi ◽  
San Martín ◽  
Basal Position

We describe Proceraea albocephala, new species, from Madeira, and Erseia oligochaeta, new genus and new species, from Istria, Croatia, and we provide redescriptions of Proceraea madeirensis (Nygren, 2004) from topotype material, and Myrianida longoprimicirrata (López, San Martín & Jimenéz, 1997) from material collected at Istria, Croatia, and Banyuls-sur-Mer, France. Proceraea albocephala, new species is morphologically separated from similar species by a prostomial white spot, and E. oligochaeta, new genus, new species is unique in having only a few (1–2) simple unidentate chaetae in all chaetigers, and a trepan with a single large and 25–28 smaller teeth. We assess the phylogenetic positions of the four species using nuclear 18SrDNA, together with mitochondrial COI and 16SrDNA. Our molecular data show that among the sequenced autolytines 1) P. albocephala, new species is most closely related to P. nigropunctata Nygren & Gidholm, 2001, P. okadai (Imajima, 1966), and P. cornuta (Agassiz, 1862), 2) E. oligochaeta, new genus, new species belongs within a clade together with Procerastea nematodes Langerhans, 1884, Virchowia clavata Langerhans, 1879, and Imajimaea draculai (San Martín & López, 2002), 3) M. longoprimicirrata is sister species to M. pentadentata (Imajima, 1966), and 4) P. madeirensis has a basal position within Procerini. The molecular data suggests that Proceraea Ehlers, 1864 as currently delineated is paraphyletic.

scholarly journals Redescription of Campoletis sonorensis (Cameron, 1886) (Hymenoptera, Ichneumonidae, Campopleginae), parasitoid of Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera, Noctuidae) in Brazil

2015 ◽  
Vol 75 (4) ◽  
pp. 989-998 ◽  
Author(s):  
L. F. Camargo ◽  
R. A. Brito ◽  
A. M. Penteado-Dias
Keyword(s):  
Biological Control ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Morphological Characters ◽  
Parasitoid Wasps ◽  
Correct Identification ◽  
Similar Species ◽  
Potential Candidate ◽  
Campoletis Sonorensis ◽  
Lepidoptera Noctuidae

Abstract The fall armyworm Spodoptera frugiperda (Lepidoptera; Noctuidae) is a voracious pest of numerous crops of economic importance throughout the New World. In Brazil, its larvae are attacked by several species of parasitoid wasps, making them potential candidate as biological control agents against this pest. A survey of the parasitoid fauna on S. frugiperda in maize crops throughout Brazil reveals two species of Campoletis, which are morphologicaly very similar species. In this paper we combine these data with pictures from the type material of C. sonorensis and C. flavicincta, as well as their descriptions to provide a redescription to Campoletis sonorensis (Cameron, 1886) using for this both morphological characters and DNA Barcoding (Hebert et al., 2003) information, in an attempt to help with the correct identification of the taxa to improve biological control studies.

The myth of monophagy in Paralobesia (Lepidoptera: Tortricidae)? A new species feeding on Cypripedium reginae (Orchidaceae)

Zootaxa ◽  
2018 ◽  
Vol 4446 (1) ◽  
pp. 81 ◽  
Author(s):  
HANNA R. ROYALS ◽  
JEAN-FRANÇOIS LANDRY ◽  
TODD M. GILLIGAN
Keyword(s):  
New Species ◽  
Feeding Habits ◽  
Dna Barcode ◽  
Molecular Data ◽  
Similar Species ◽  
Genital Morphology ◽  
Systematic Revision ◽  
Morphological And Molecular Data ◽  
Two Populations ◽  
A New Species

The genus Paralobesia Obraztsov, 1953 is found primarily in eastern North America and consists of 18 described and several undescribed species. Prior to 1900, all North American Paralobesia were assumed to be P. viteana (Clemens). However, rearing experiments by William Kearfott in the early 1900s suggested that species of Paralobesia were monophagous and could be separated by host. Recently, a species of Paralobesia was reared from showy lady’s slipper, Cypripedium reginae Walter (Orchidaceae), during a study of two populations of this orchid in eastern Ontario and southwestern Québec. Although originally assumed to be P. cypripediana (Forbes), which was described from specimens reared from Cypripedium in Manitoba, DNA barcode data and genital morphology confirmed that this was a new species similar to P. cypripediana and P. monotropana (Heinrich). Herein, we describe P. marilynae, sp. n., and provide specifics of its discovery and life history. Rearing records indicate that Paralobesia can span the range from strictly monophagous to polyphagous, even for very similar species with similar feeding habits, and that host records should be combined with morphological and molecular data when circumscribing species in this genus. This work is part of a complete systematic revision of Paralobesia currently in progress. 

scholarly journals Machine Learning Models with Quantitative Wood Anatomy Data Can Discriminate between Swietenia macrophylla and Swietenia mahagoni

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 36 ◽  
Author(s):  
Tuo He ◽  
João Marco ◽  
Richard Soares ◽  
Yafang Yin ◽  
Alex Wiedenhoeft
Keyword(s):  
Machine Learning ◽  
Wood Anatomy ◽  
Support Vector ◽  
Correct Identification ◽  
Similar Species ◽  
Learning Models ◽  
Important Species ◽  
Quantitative Wood Anatomy ◽  
Depth Analysis ◽  
Machine Learning Models

Illegal logging and associated trade aggravate the over-exploitation of Swietenia species, of which S. macrophylla King, S. mahagoni (L.) Jacq, and S. humilis Zucc. have been listed in Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Appendix Ⅱ. Implementation of CITES necessitates the development of efficient forensic tools to identify wood species accurately, and ideally ones readily deployable in wood anatomy laboratories across the world. Herein, a method using quantitative wood anatomy data in combination with machine learning models to discriminate between three Swietenia species is presented, in addition to a second model focusing only on the two historically more important species S. mahagoni and S. macrophylla. The intra- and inter-specific variations in nine quantitative wood anatomical characters were measured and calculated based on 278 wood specimens, and four machine learning classifiers—Decision Tree C5.0, Naïve Bayes (NB), Support Vector Machine (SVM), and Artificial Neural Network (ANN)—were used to discriminate between the species. Among these species, S. macrophylla exhibited the largest intraspecific variation, and all three species showed at least partly overlapping values for all nine characters. SVM performed the best of all the classifiers, with an overall accuracy of 91.4% and a per-species correct identification rate of 66.7%, 95.0%, and 80.0% for S. humilis, S. macrophylla, and S. mahagoni, respectively. The two-species model discriminated between S. macrophylla and S. mahagoni with accuracies of over 90.0% using SVM. These accuracies are lower than perfect forensic certainty but nonetheless demonstrate that quantitative wood anatomy data in combination with machine learning models can be applied as an efficient tool to discriminate anatomically between similar species in the wood anatomy laboratory. It is probable that a range of previously anatomically inseparable species may become identifiable by incorporating in-depth analysis of quantitative characters and appropriate statistical classifiers.

scholarly journals Data science competition for cross-site delineation and classification of individual trees from airborne remote sensing data

2021 ◽  
Author(s):  
Sarah J Graves ◽  
Sergio Marconi ◽  
Dylan Stewart ◽  
Ira Harmon ◽  
Ben G Weinstein ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Data Science ◽  
Remote Sensing Data ◽  
Common Species ◽  
Gradient Boosting ◽  
Individual Species ◽  
Site Classification ◽  
Similar Species ◽  
Sensing Data ◽  
Individual Trees

Delineating and classifying individual trees in remote sensing data is challenging. Many tree crown delineation methods have difficulty in closed-canopy forests and do not leverage multiple datasets. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for delineation of individual crowns and classification to determine species identity. This competition included data from multiple sites to assess the methods' ability to generalize learning across multiple sites simultaneously, and transfer learning to novel sites where the methods were not trained. Six teams, representing 4 countries and 9 individual participants, submitted predictions. Methods from a previous competition were also applied and used as the baseline to understand whether the methods are changing and improving over time. The best delineation method was based on an instance segmentation pipeline, closely followed by a Faster R-CNN pipeline, both of which outperformed the baseline method. However, the baseline (based on a growing region algorithm) still performed well as did the Faster R-CNN. All delineation methods generalized well and transferred to novel forests effectively. The best species classification method was based on a two-stage fully connected neural network, which significantly outperformed the baseline (a random forest and Gradient boosting ensemble). The classification methods generalized well, with all teams training their models using multiple sites simultaneously, but the predictions from these trained models generally failed to transfer effectively to a novel site. Classification performance was strongly influenced by the number of field-based species IDs available for training the models, with most methods predicting common species well at the training sites. Classification errors (i.e., species misidentification) were most common between similar species in the same genus and different species that occur in the same habitat. The best methods handled class imbalance well and learned unique spectral features even with limited data. Most methods performed better than baseline in detecting new (untrained) species, especially in the site with no training data. Our experience further shows that data science competitions are useful for comparing different methods through the use of a standardized dataset and set of evaluation criteria, which highlights promising approaches and common challenges, and therefore advances the ecological and remote sensing field as a whole.

scholarly journals Herbal Mixtures: Aspects Related to the Quality of Chinese Medicine Formulas and Perspectives for Products Registration in Brazil

2021 ◽  
pp. 28-45
Author(s):  
Ferdinando Lucas Góis ◽  
Ademir Evangelista Do Vale ◽  
Gislane Oliveira Ribeiro ◽  
Erika Maria de Oliveira Ribeiro
Keyword(s):  
Chinese Medicine ◽  
Traditional Medicine ◽  
Pharmaceutical Care ◽  
Herbal Medicines ◽  
World Health ◽  
Individual Species ◽  
Correct Identification ◽  
Chemical Complexity ◽  
The World ◽  
Herbal Mixtures

Traditional medicine products are easily found in different regions of the world. Given this scenario, the World Health Organization (WHO) is very interested in the rational insertion of these resources, especially in primary pharmaceutical care in emerging countries. One of the main concerns of the WHO is with the population's access to traditional medicine products without quality guaranteed by regulatory and health control agencies in the country of origin. In ancient Chinese Pharmacology and Medicine, products based on associated drugs, used by boiling in water (decoction), successfully contribute to maintaining the health of Chinese people. In Brazil, the sanitary legislation of herbal mixtures for medicinal teas allows the sanitary notification of these products as traditional herbal medicines. On the other hand, the lack of clinical services to monitor consumption and the scarcity of evidence to ensure safety and efficacy, add to the inadequacy of the products to sanitary standards, the lack of inspection, and the definition of quality parameters for the evaluation of mixtures. Due to the chemical complexity of herbal mixtures, the correct identification of drugs through conventional techniques is usually possible for individual species, making it necessary to develop more comprehensive approaches. These testes allow to investigate the presence and/or absence of multiple pre-established markers, through the concept of fingerprint similarity and evaluation by chemometric tools. Liquid chromatography integrated with mass spectrometry and multivariate data analysis proved to be the most used method. Among the objectives of this critical and prospective review are: to describe the probable origin of medicinal teas, the theoretical foundation of the compositions in pharmacology and traditional Chinese medicine, the modern techniques developed in the quality control of herbal mixtures, and the perspectives for rational and safe insertion of traditional herbal medicines in Brazilian pharmaceutical care.

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