scholarly journals Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

2017 ◽  
Author(s):  
Marcio R. Pie ◽  
Marcos R. Bornschein ◽  
Luiz F. Ribeiro ◽  
Brant C. Faircloth ◽  
John E. McCormack
Keyword(s):  
Atlantic Forest ◽  
Species Delimitation ◽  
Large Scale ◽  
Sensitivity Analyses ◽  
Brazilian Atlantic Forest ◽  
Sky Islands ◽  
Relative Contribution ◽  
Locus Selection ◽  
Current Species ◽  
Generation Sequencing

AbstractThe advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness, such as those with higher numbers of parsimony-informative sites. Here, we explore the issue of species delimitation and locus selection with species from two anuran genera: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). Montane species in these genera have been isolated in sky islands across the southern Brazilian Atlantic Forest, which led to the formation of a number of microendemic species. To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their corresponding number of parsimony-informative sites, and we performed species delimitation analyses using BPP in each genus based on the top 10, 20, 40, 80, 160, 320, and 640 loci. We also conducted several additional analyses using 10 randomly sampled datasets containing the same numbers of loci to discriminate the relative contribution of increasing the number of loci from prioritizing those with higher informativeness. We identified three types of node: nodes with either consistently high or low support regardless of the number of loci or their informativeness, and nodes that were initially poorly supported, but their support became stronger with more data. Adding more loci had a stronger impact on model support than prioritizing loci for their informativeness, but this effect was less apparent in datasets with more than 160 loci. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera might have been underestimated. In addition, our results provide useful guidelines to the use of different sampling strategies to carry out species delimitation with phylogenomic datasets.

scholarly journals Phylogenomics of montane frogs of the Brazilian Atlantic Forest supports a scenario of isolation in sky islands followed by relative climatic stability

2017 ◽  
Author(s):  
Marcio R. Pie ◽  
Brant C. Faircloth ◽  
Luiz F. Ribeiro ◽  
Marcos R. Bornschein ◽  
John E. McCormack
Keyword(s):  
Species Diversity ◽  
Atlantic Forest ◽  
Geographical Area ◽  
Bootstrap Support ◽  
Brazilian Atlantic Forest ◽  
Sky Islands ◽  
Evolutionary Mechanisms ◽  
Target Capture ◽  
Divergence Dating ◽  
Individual Trees

AbstractDespite encompassing a relatively small geographical area, montane regions harbor disproportionately high levels of species diversity and endemism. Yet, relatively little is known about the evolutionary mechanisms ultimately leading to montane diversity. In this study, we use target capture of ultraconserved elements to investigate the phylogenetic relationships and diversification patterns of Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae), two frog genera that occur in sky islands of the southern Atlantic Forest of Brazil. Specifically, we test whether diversification of montane species in these genera can be explained by a single climatic shift leading to isolation in sky islands, followed by relative climatic stability that maintained populations in allopatry. In both genera, the topologies inferred using concatenation and coalescent-based methods were concordant and had strong nodal support, except for a few recent splits. These recent splits tended to be supported by more informative loci (those with higher average bootstrap support), suggesting that, while individual trees may be well resolved, the relationships they recover are being obscured by non-informative data. Divergence dating of a combined dataset using both genera is consistent with concordant timing of their diversification. These results support the scenario of diversification-by-isolation in sky islands, and suggest that allopatry due to climatic gradients in montane regions are an important mechanism for generating species diversity and endemism in these regions.

scholarly journals Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

2019 ◽  
Vol 141 ◽  
pp. 106627 ◽  
Author(s):  
Marcio R. Pie ◽  
Marcos R. Bornschein ◽  
Luiz F. Ribeiro ◽  
Brant C. Faircloth ◽  
John E. McCormack
Keyword(s):  
Atlantic Forest ◽  
Species Delimitation ◽  
Brazilian Atlantic Forest

scholarly journals The relative contribution of fruits and arthropods to the diet of three trogon species (Aves, Trogonidae) in the Brazilian Atlantic Forest

2007 ◽  
Vol 24 (2) ◽  
pp. 515-517 ◽  
Author(s):  
Marco Aurélio Pizo
Keyword(s):  
Social Behavior ◽  
Tropical Forest ◽  
Atlantic Forest ◽  
Forest Birds ◽  
Brazilian Atlantic Forest ◽  
Food Items ◽  
Relative Contribution ◽  
Direct Observations ◽  
Dry Seasons ◽  
Wet And Dry Seasons

Trogons are pan-tropical forest birds that eat a mix of fruits and arthropods. With direct observations of wild feeding birds, I assessed the relative contribution of fruits and arthropods to the diet of three trogon species (Trogonviridis, T.surrucura, and T.rufus) at Parque Estadual Intervales, southeast Brazil. Fruits and arthropods made the bulk of the food items recorded, with a tendency of frugivory increasing with body mass. The Trogon species differed in the proportion of fruits and arthropods taken, with T.viridis being the most frugivorous species (66% of feeding bouts, n = 47). The relative contribution of fruits and arthropods did not differ between the wet and dry seasons for any species. In the omnivorous gradient, T.viridis is close to the frugivorous extreme, whereas T.surrucura and T.rufus is next to the insectivorous end. Such a distinction may have important consequences for the territoriality and social behavior of these birds.

scholarly journals Insights from a large-scale inventory in the southern Brazilian Atlantic Forest

2020 ◽  
Vol 77 (1) ◽  
Author(s):  
Alexander Christian Vibrans ◽  
André Luís de Gasper ◽  
Paolo Moser ◽  
Laio Zimermann Oliveira ◽  
Débora Vanessa Lingner ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Large Scale ◽  
Brazilian Atlantic Forest

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

The centipede genus Otostigmus Porat in Brazil: Description of three new species from the Atlantic Forest; a summary and an identification key to the Brazilian species of this genus (Chilopoda, Scolopendromorpha, Scolopendridae, Otostigminae)

Zootaxa ◽  
2012 ◽  
Vol 3280 (1) ◽  
pp. 1 ◽  
Author(s):  
AMAZONAS CHAGAS-JÚNIOR
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
The State ◽  
Junior Synonym ◽  
Identification Key ◽  
Nominal Species ◽  
Brazilian Atlantic Forest ◽  
Three New Species ◽  
First Time ◽  
New Distribution

Three new species of Otostigmus Porat, 1876 from Brazilian Atlantic Forest are described. Otostigmus beckeri sp. n. andO. lanceolatus sp. n. are described from the state of Bahia and O. giupponii sp. n. from the state of Espírito Santo. InBrazil, the otostigmine scolopendrid genus Otostigmus comprises 22 species. A summary of Brazilian Otostigmus speciesis presented with new distribution records, taxonomic remarks when appropriate and an identification key. Otostigmus sul-catus Meinert, 1886 is recorded for the first time from Brazil; the Andean Otostigmus silvestrii Kraepelin 1903, previouslyrecorded from Brazil, is here considered not to be present in this country. Eight nominal species are regarded here as newsynonyms. Five of them—Otostigmus pradoi Bücherl, 1939, O. longistigma Bücherl, 1939, O. longipes Bücherl, 1939,O. langei Bücherl, 1946 and O. dentifusus Bücherl, 1946—are based on females of O. tibialis Brölemann, 1902. O. latipesBücherl, 1954 is conspecific with and is considered a junior synonym of O. sulcatus Meinert, 1886; O. limbatus diminutusBücherl, 1946 is a junior synonym of O. limbatus Meinert, 1886 and O. fossulatus Attems, 1928 is a junior synonym of O. goeldii Brölemann, 1898. A lectotype is designated for O. goeldii.

scholarly journals Strategic resources and smallholder performance at the bottom of the pyramid

2019 ◽  
Vol 22 (3) ◽  
pp. 365-380 ◽  
Author(s):  
Matthias Olthaar ◽  
Wilfred Dolfsma ◽  
Clemens Lutz ◽  
Florian Noseleit
Keyword(s):  
Large Scale ◽  
Business Environment ◽  
Agricultural Economics ◽  
Local Market ◽  
Bottom Of The Pyramid ◽  
Fine Grained ◽  
Strategic Resources ◽  
Relative Contribution ◽  
The Relationship ◽  
Resource Based Theory

In a competitive business environment at the Bottom of the Pyramid smallholders supplying global value chains may be thought to be at the whims of downstream large-scale players and local market forces, leaving no room for strategic entrepreneurial behavior. In such a context we test the relationship between the use of strategic resources and firm performance. We adopt the Resource Based Theory and show that seemingly homogenous smallholders deploy resources differently and, consequently, some do outperform others. We argue that the ‘resource-based theory’ results in a more fine-grained understanding of smallholder performance than approaches generally applied in agricultural economics. We develop a mixed-method approach that allows one to pinpoint relevant, industry-specific resources, and allows for empirical identification of the relative contribution of each resource to competitive advantage. The results show that proper use of quality labor, storage facilities, time of selling, and availability of animals are key capabilities.

scholarly journals Hide-and-Seek with Tiny Neotenic Beetles in One of the Hottest Biodiversity Hotspots: Towards an Understanding of the Real Diversity of Jurasaidae (Coleoptera: Elateroidea) in the Brazilian Atlantic Forest

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 420
Author(s):  
Gabriel Biffi ◽  
Simone Policena Rosa ◽  
Robin Kundrata
Keyword(s):  
Atlantic Forest ◽  
Field Research ◽  
Transitional Zone ◽  
Biodiversity Hotspot ◽  
Biodiversity Hotspots ◽  
Brazilian Atlantic Forest ◽  
Life Stages ◽  
Adult Males ◽  
Undescribed Species ◽  
First Time

Jurasaidae are a family of neotenic elateroid beetles which was described recently from the Brazilian Atlantic Forest biodiversity hotspot based on three species in two genera. All life stages live in the soil, including the larviform females, and only adult males are able to fly. Here, we report the discovery of two new species, Jurasai miraculum sp. nov. and J. vanini sp. nov., and a new, morphologically remarkable population of J. digitusdei Rosa et al., 2020. Our discovery sheds further light on the diversity and biogeography of the group. Most species of Jurasaidae are known from the rainforest remnants of the Atlantic Forest, but here for the first time we report a jurasaid species from the relatively drier Atlantic Forest/Caatinga transitional zone. Considering our recent findings, minute body size and cryptic lifestyle of all jurasaids, together with potentially high numbers of yet undescribed species of this family from the Atlantic Forest and possibly also other surrounding ecoregions, we call for both field research in potentially suitable localities as well as for a detailed investigation of a massive amount of already collected but still unprocessed materials deposited in a number of Brazilian institutes, laboratories and collections.

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