scholarly journals Sky islands of the Cameroon Volcanic Line support the westernmost clade of five new Typoderus weevils (Coleoptera: Curculionidae: Molytinae)

2021 ◽  
Vol 79 ◽  
pp. 57-74
Author(s):  
Vasily V. Grebennikov
Keyword(s):  
Molecular Clock ◽  
Dna Barcode ◽  
Temporal Analysis ◽  
Congo Basin ◽  
Supplementary Information ◽  
Sky Islands ◽  
Fixed Rate ◽  
Climatic Fluctuations ◽  
Cameroon Volcanic Line ◽  
Mt Kupe

Abstract The weevil genus Typoderus is for the first time reported west of the Congo basin. Analysis of 2,136 aligned positions from one mitochondrial and two nuclear fragments revealed a moderately supported clade of five new Cameroonian species: T. amphionsp. nov. (Mt. Oku), T. canthussp. nov. (Mt. Oku), T. clytiussp. nov. (Mt. Cameroon), T. iphitussp. nov. (Mt. Kupe) and T. telamonsp. nov. (Mt. Kupe). Molecular clock analysis of 20 DNA barcode fragments using a fixed substitution rate estimated divergences within this clade to be during the Middle to Late Miocene (10.5–5.4 million years ago, MYA), which pre-dates the onset of the Pliocene-Pleistocene global climatic fluctuations and corresponding cycles of African forest size fluctuation. Such relatively old dates are unexpected and might reflect four unavoidable shortcomings of the temporal analysis: 1. undersampled ingroup, 2. scarcity of comparative temporal data for other animal clades from the Cameroon Volcanic Line, 3. oversimplification of a fixed-rate molecular clock approach using a single maternally-inherited protein-coding marker and 4. possible overestimation of comparatively old ages when using largely saturated mitochondrial sequences. Two obscure weevil species from the Republic of the Congo are hypothesized to belong to the genus Typoderus: T. distinctus (Hoffmann, 1968) comb. nov. (from Anchonidium subgenus Neoanchonidium) and T. baloghi (Hoffmann, 1968) comb. nov. (from Anchonidium subgenus Subanchonidium). Three genus-group names are newly synonymized under Typoderus: Entypoderus Voss, 1965 syn. nov. (the only non-nominative subgenus of Typoderus), Neoanchonidium Hoffmann, 1968 syn. nov. (subgenus of Anchonidium) and Subanchonidium Hoffmann, 1968 syn. nov. (subgenus of Anchonidium). Habitus images and other supplementary information of all sequenced specimens are available online at dx.doi.org/10.5883/DS-VGDS005 and dx.doi.org/10.5883/DS-VGDS006.

scholarly journals Detecting turnover among complex communities using null models: A case study with sky-island haemosporidian parasites

2020 ◽  
Author(s):  
Lisa N. Barrow ◽  
Selina M. Bauernfeind ◽  
Paxton A. Cruz ◽  
Jessie L. Williamson ◽  
Daniele L. Wiley ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Dna Barcode ◽  
Biotic Interactions ◽  
Null Models ◽  
Sky Islands ◽  
Mountain Ranges ◽  
Haemosporidian Parasites ◽  
Community Turnover ◽  
The One ◽  
Sky Island

AbstractTurnover in species composition between sites, or beta diversity, is a critical component of species diversity that is typically influenced by geography, environment, and biotic interactions. Quantifying turnover is particularly challenging, however, in multi-host, multi-parasite assemblages where undersampling is unavoidable, resulting in inflated estimates of turnover and uncertainty about its spatial scale. We developed and implemented a framework using null models to test for community turnover in avian haemosporidian communities of three sky islands in the southwestern United States. We screened 776 birds for haemosporidian parasites from three genera (Parahaemoproteus, Plasmodium, and Leucocytozoon) by amplifying and sequencing a mitochondrial DNA barcode. We detected infections in 280 birds (36.1%), sequenced 357 infections, and found a total of 99 parasite haplotypes. When compared to communities simulated from a regional pool, we observed more unique, single-mountain haplotypes and fewer haplotypes shared among three mountain ranges than expected, indicating that haemosporidian communities differ to some degree among adjacent mountain ranges. These results were robust even after pruning datasets to include only identical sets of host species, and they were consistent for two of the three haemosporidian genera. The two more distant mountain ranges were more similar to each other than the one located centrally, suggesting that the differences we detected were due to stochastic colonization-extirpation dynamics. These results demonstrate that avian haemosporidian communities of temperate-zone forests differ on relatively fine spatial scales associated with adjacent sky-islands. Null models are essential tools for detecting turnover in complex, undersampled, and poorly known systems.

scholarly journals Phylogeography and sister group of Lupangus, a new genus for three new flightless allopatric forest litter weevils endemic to the Eastern Arc Mountains, Tanzania (Coleoptera: Curculionidae, Molytinae)

2017 ◽  
Vol 49 (1) ◽  
pp. 37 ◽  
Author(s):  
Vasily V. Grebennikov
Keyword(s):  
Type Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Forest Litter ◽  
Temporal Analysis ◽  
Sister Group ◽  
Eastern Arc Mountains ◽  
Climatic Fluctuations ◽  
Mitochondrial Coi ◽  
Eastern Arc

This paper reports discovery of a new genus <em>Lupangus</em> gen. n. with three new flightless weevils endemic to the forests of the Eastern Arc Mountains in Tanzania: <em>L. asterius</em> sp. n. (East Usambara; the type species), <em>L. jason</em> sp. n. (Uluguru) and<em> L. orpheus</em> sp. n. (Udzungwa). Maximum Likelihood phylogenetic analyses using parts of mitochondrial (COI), nuclear ribosomal (28S) genes, as well as the nuclear spacer region (ITS2) from 46 terminals grouped together the reciprocally monophyletic <em>Lupangus</em> (3 terminals) and <em>Typoderus</em> (3 terminals), with all three clades strongly supported. Phylogenetic analysis of 32 COI-5’ sequences recovered <em>Lupangus</em> species as reciprocally monophyletic, with <em>L</em>. <em>orpheus</em> being the sister to the rest. Internal phylogeny within both <em>L. jason</em> and <em>L.</em> <em>orpheus</em> are geographically structured, while that of <em>L. asterius</em> is not. Temporal analysis of <em>Lupangus</em> evolution using COI-5’ data assessed under slow and fast substitution rate schemes estimated separation of mitochondrial lineages leading to three <em>Lupangus</em> species at about 7–8 Ma and about 1.9–2.1 Ma, respectively. Temporal analyses consistently failed to suggest correlation between the timing of <em>Lupangus</em> evolution and the late Pleistocene climatic fluctuations, thus rejecting the hypothesis of faunal interchanges during the wettest periods of the last million years. Applicability of flightless weevils for dispersal-vicariance analysis is reviewed, and their mostly undocumented and taxonomically entangled diversity in the Tanzanian Eastern Arc Mountains is briefly highlighted.

scholarly journals Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin

2020 ◽  
Vol 7 (3) ◽  
pp. 191582 ◽  
Author(s):  
Frederik Van de Perre ◽  
Michael R. Willig ◽  
Steven J. Presley ◽  
Itoka Jean-Claude Mukinzi ◽  
Mbalitini Sylvestre Gambalemoke ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Assembly ◽  
Species Coexistence ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Congo Basin ◽  
Climatic Fluctuations ◽  
Fundamental Goal ◽  
Vicariance Event ◽  
Lowland Forests

Understanding the determinants of species coexistence in complex and species-rich communities is a fundamental goal of ecology. Patterns of species coexistence depend on how biotic interactions and environmental filtering act over ecological and evolutionary time scales. Climatic fluctuations in lowland rainforests of the Congo Basin led to the number of vertebrate species being significantly lower in central compared with northern ecoregions of the Basin. We used null models to assess whether climatic variations affected the community assembly of shrews. A consistent limit to functional similarity of species was not related to species richness. Rather, species richness is constrained by environmental factors, and these constraints are stronger in the central lowland forests of the Congo Basin. By constraining species geographic distributions, historical effects of rainforest refugia arising from climatic fluctuations may affect contemporary species composition of local shrew communities. The Congo River represents a vicariance event that led to allopatric speciation of shrews and continues to represent a barrier to dispersal. Ultimately, the historical effects of this barrier have led to differences in the functional volume of shrew communities in northern and central ecoregions. We suggest that the analyses of community assembly can be used to identify Holocene refugia in the Congo Basin.

scholarly journals DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments

2018 ◽  
Vol 35 (15) ◽  
pp. 2690-2691 ◽  
Author(s):  
Céline Trébeau ◽  
Jacques Boutet de Monvel ◽  
Fabienne Wong Jun Tai ◽  
Christine Petit ◽  
Raphaël Etournay
Keyword(s):  
User Interfaces ◽  
Dna Barcode ◽  
R Package ◽  
Supplementary Information ◽  
Minimal Distance ◽  
Source Codes ◽  
Dna Library ◽  
Core Facilities ◽  
User Friendly ◽  
Multiplex Sequencing

Abstract Summary Using adequate DNA barcodes is essential to unambiguously identify each DNA library within a multiplexed set of libraries sequenced using next-generation sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one to design single or dual-barcoding multiplex experiments by imposing desired constraints on the barcodes (including sequencer chemistry, barcode pairwise minimal distance and nucleotide content), while optimizing barcode frequency usage, thereby allowing one to both facilitate the demultiplexing step and spare expensive library-preparation kits. The package comes with a user-friendly interface and a web app developed in Java and Shiny (https://dnabarcodecompatibility.pasteur.fr), respectively, with the aim to help bridge the expertise of core facilities with the experimental needs of non-experienced users. Availability and implementation DNABarcodeCompatibility can be easily extended to fulfil specific project needs. The source codes of the R-package and its user interfaces are publicly available along with documentation at [https://github.com/comoto-pasteur-fr] under the GPL-2 licence. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Mitochondrial substitution rates estimation for molecular clock analyses in modern birds based on full mitochondrial genomes

2019 ◽  
Author(s):  
Angel Arcones ◽  
Raquel Ponti ◽  
David R. Vieites
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Clock ◽  
Bird Species ◽  
Divergence Times ◽  
Mitochondrial Genomes ◽  
Fixed Rate ◽  
D Loop ◽  
Standard Clock ◽  
Complete Mitochondrial Genomes ◽  
Mtdna Marker

AbstracttiMitochondrial DNA (mtDNA) is a very popular resource in the study of evolutionary processes in birds, and especially to infer divergence times between lineages. These inferences rely on rates of substitution in the mtDNA genes that, ideally, are specific for the studied taxa. But as such values are often unavailable many studies fixed rate values generalised from other studies, such as the popular “standard molecular clock”. However the validity of these universal rates across all bird lineages and for the different mtDNA has been severely questioned. Thus, we here performed the most comprehensive calibration of the mtDNA molecular clock in birds, with the inclusion of complete mitochondrial genomes for 622 bird species and 25 reliable fossil calibrations. The results show variation in the rates between lineages and especially between markers, contradicting the universality of the standard clock. Moreover, we provide especific rates for every mtDNA marker (except D-loop) in each of the sampled avian orders, which should help improve future estimations of divergence times between bird species or populations.

Twitter Usage Using Common Reference to Tinnitus

2020 ◽  
Vol 29 (2) ◽  
pp. 206-217
Author(s):  
Jianyuan Ni ◽  
Monica L. Bellon-Harn ◽  
Jiang Zhang ◽  
Yueqing Li ◽  
Vinaya Manchaiah
Keyword(s):  
Nonprofit Organizations ◽  
Temporal Trends ◽  
Temporal Analysis ◽  
Cross Sectional ◽  
For Profit ◽  
Common Reference ◽  
Personal Experiences ◽  
Twitter Users ◽  
Sectional Analysis ◽  
Share Information

Objective The objective of the study was to examine specific patterns of Twitter usage using common reference to tinnitus. Method The study used cross-sectional analysis of data generated from Twitter data. Twitter content, language, reach, users, accounts, temporal trends, and social networks were examined. Results Around 70,000 tweets were identified and analyzed from May to October 2018. Of the 100 most active Twitter accounts, organizations owned 52%, individuals owned 44%, and 4% of the accounts were unknown. Commercial/for-profit and nonprofit organizations were the most common organization account owners (i.e., 26% and 16%, respectively). Seven unique tweets were identified with a reach of over 400 Twitter users. The greatest reach exceeded 2,000 users. Temporal analysis identified retweet outliers (> 200 retweets per hour) that corresponded to a widely publicized event involving the response of a Twitter user to another user's joke. Content analysis indicated that Twitter is a platform that primarily functions to advocate, share personal experiences, or share information about management of tinnitus rather than to provide social support and build relationships. Conclusions Twitter accounts owned by organizations outnumbered individual accounts, and commercial/for-profit user accounts were the most frequently active organization account type. Analyses of social media use can be helpful in discovering issues of interest to the tinnitus community as well as determining which users and organizations are dominating social network conversations.

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