scholarly journals Hydrography rather than lip morphology better explains the evolutionary relationship between Gymnogeophagus labiatus and G. lacustris in Southern Brazil (Cichlidae: Geophagini)

2021 ◽  
Vol 19 (4) ◽  
Author(s):  
Pedro Ivo C. C. Figueiredo ◽  
Luiz R. Malabarba ◽  
Nelson J. R. Fagundes
Keyword(s):  
Coastal Lagoons ◽  
Evolutionary Relationship ◽  
Genetic Lineage ◽  
Data Sets ◽  
Patos Lagoon ◽  
Hydrographic Basin ◽  
Ecological Requirements ◽  
Evolutionary Lineages ◽  
Male Coloration ◽  
Sand Bottom

ABSTRACT Gymnogeophagus labiatus and G. lacustris have been long recognized as sister species exhibiting different ecological requirements. Gymnogeophagus labiatus occurs in rock bottom rivers in the hydrographic basins of Patos Lagoon (HBP) and Tramandaí River (HBT), while G. lacustris is exclusive from sand bottom coastal lagoons of the HBT. In this study, we used molecular markers, morphological measurements and data from nuptial male coloration to investigate the evolutionary relationship between these species in each hydrographic basin. We found, for all data sets, a closer relationship between G. labiatus and G. lacustris from the HBT than between G. labiatus populations from HBT and HBP. In particular, lip area had a large intraspecific plasticity, being uninformative to diagnose G. lacustris from G. labiatus. Molecular clock-based estimates suggest a recent divergence between species in the HBT (17,000 years ago), but not between G. labiatus from HBP and HBT (3.6 millions of years ago). Finally, we also found a divergent G. labiatus genetic lineage from the Camaquã River, in the HBP. These results show that the current taxonomy of G. labiatus and G. lacustris does not properly represent evolutionary lineages in these species.

scholarly journals Molecular and Phylogenetic Analysis of Family Aeshnidae of Hazara Region, Pakistan

2021 ◽  
Vol 25 (01) ◽  
pp. 109-116
Author(s):  
Sardar Azhar Mehmood
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Rate ◽  
Evolutionary Relationship ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Bootstrap Support ◽  
Data Sets ◽  
Data Set ◽  
Single Genus ◽  
Shared Genetic

Current study was conducted on family Aeshnidae from Hazara region of Pakistan. During the survey a total of 125 members were collected and identified into 2 species under single genus. The present study focuses on molecular characterizations and phylogenetics of family Aeshnidae. Phylogenies of the analyzed taxa were elaborated with maximum likelihood, maximum parsimony and Bayesian analysis. We sequenced both mitochondrial genes i.e., COI and 16S rRNA, separate and combined CO1+16S data sets revealed evolutionary relationship within Aeshnidae at the species and genera level. Mean Pairwise Distances (MPD) of each species were ranged from 0.00 to 84.60%. Evolutionary rate differences among two categories Gamma distribution and Invariant were recorded as 0.07 and 1.20 substitutions per site. DNA based identification using CO1, 16S and combined CO1+16S data set, for all Aeshnidae species shared genetic similarities having bootstrap values MLB=70–100%, MPB= 52–100% and BPP=0.75–1% respectively. The analysis of the combined (COI+16S) data set produced trees with complete stronger bootstrap support than analyses of either gene alone. These findings had shown that the taxonomic position of Aeshnidae species based on morphological characters could be verified, further improved and confirmed by the use of modern molecular biological tools which involve the nucleotide sequences of genes used in phylogenetic investigations. © 2021 Friends Science Publishers

scholarly journals Evidence of habitat fragmentation affecting fish movement between the Patos and Mirim coastal lagoons in southern Brazil

2006 ◽  
Vol 4 (1) ◽  
pp. 69-72 ◽  
Author(s):  
Marcelo D. M. Burns ◽  
Alexandre M. Garcia ◽  
João P. Vieira ◽  
Marlise A. Bemvenuti ◽  
David M. L. Motta Marques ◽  
...  
Keyword(s):  
Coastal Lagoons ◽  
Patos Lagoon ◽  
White Croaker ◽  
Estuarine Fishes ◽  
Patos Lagoon Estuary ◽  
Salinity Water ◽  
Study Sites ◽  
Natural Channel ◽  
Odontesthes Argentinensis ◽  
Lagoon Systems

The communication between the Patos and Mirim lagoon systems occurs via a natural channel called São Gonçalo. In 1977, a dam was built in this channel to prevent entrance of saline waters from Patos Lagoon estuary into the Mirim Lagoon. Our results showed an abrupt discontinuity in salinity and fish species distribution along the study sites. Sites below the dam showed salinity values higher than zero, whereas sites above had zero salinity values across all sampling periods. Marine and estuarine fishes (e.g., mullets Mugil platanus, M. curema, silversides Odontesthes argentinensis, Atherinella brasiliensis, sardine Brevoortia pectinata, and white croaker Micropogonias furnieri) were not captured above the dam. If these juvenile fishes could enter the Mirim lagoon in greater numbers, they probably would enhance catches in the artisanal fishery. We hypothesized that the São Gonçalo dam acts as a barrier hindering the entrance of salinity water and fishes inside the Mirim Lagoon.

scholarly journals Complex Molecular Relationship Between Vegetative Compatibility Groups (VCGs) in Verticillium dahliae: VCGs Do Not Always Align with Clonal Lineages

2014 ◽  
Vol 104 (6) ◽  
pp. 650-659 ◽  
Author(s):  
María del Mar Jiménez-Gasco ◽  
Glenna M. Malcolm ◽  
Mónica Berbegal ◽  
Josep Armengol ◽  
Rafael M. Jiménez-Díaz
Keyword(s):  
Verticillium Dahliae ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Intergenic Spacer ◽  
Vegetative Compatibility ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Vegetative Compatibility Groups ◽  
Intergenic Spacer Region ◽  
Phylogenetic Lineages

Verticillium wilts caused by the soilborne fungus Verticillium dahliae are among the most challenging diseases to control. Populations of this pathogen have been traditionally studied by means of vegetative compatibility groups (VCGs) under the assumption that VCGs comprise genetically related isolates that correlate with clonal lineages. We aimed to resolve the phylogenetic relationships among VCGs and their subgroups based on sequences of the intergenic spacer region (IGS) of the ribosomal DNA and six anonymous polymorphic sequences containing single-nucleotide polymorphisms (VdSNPs). A collection of 68 V. dahliae isolates representing the main VCGs and subgroups (VCGs 1A, 1B, 2A, 2B, 3, 4A, 4B, and 6) from different geographic origins and hosts was analyzed using the seven DNA regions. Maximum parsimony (MP) phylogenies inferred from IGS and VdSNP sequences showed five and six distinct clades, respectively. Phylogenetic analyses of individual and combined data sets indicated that certain VCG subgroups (e.g., VCGs 1A and 1B) are closely related and share a common ancestor; however, other subgroups (e.g., VCG 4B) are more closely related to members of a different VCG (e.g., VCG 2A) than to subgroups of the same VCG (VCG 4B). Furthermore, MP analyses indicated that VCG 2B is polyphyletic, with isolates placed in at least three distinct phylogenetic lineages based on IGS sequences and two lineages based on VdSNP sequences. Results from our study suggest the existence of main VCG lineages that contain VCGs 1A and 1B; VCGs 2A and 4B; and VCG 4A, for which both phylogenies agree; and the existence of other VCGs or VCG subgroups that seem to be genetically heterogeneous or show discrepancies in their phylogenetic placement: VCG 2B, VCG 3, and VCG 6. These results raise important caveats regarding the interpretation of VCG analyses: genetic homogeneity and close evolutionary relationship between members of a VCG should not be assumed.

Assessing effects of genetic, environmental, and biotic gradients in species distribution modelling

2019 ◽  
Vol 76 (6) ◽  
pp. 1762-1775 ◽  
Author(s):  
J Benjamin Lowen ◽  
Devorah R Hart ◽  
Ryan R E Stanley ◽  
Sarah J Lehnert ◽  
Ian R Bradbury ◽  
...  
Keyword(s):  
Species Distribution ◽  
Prediction Error ◽  
Total Error ◽  
Genetic Lineage ◽  
Prediction Errors ◽  
Biotic Interaction ◽  
Biological Unit ◽  
Genetic Lineages ◽  
Sea Scallop ◽  
Ecological Requirements

Abstract To develop more reliable marine species distribution models (SDMs), we examine how genetic, climatic, and biotic interaction gradients give rise to prediction error in marine SDM. Genetic lineages with distinct ecological requirements spanning genetic gradients have yet to be treated separately in marine SDM, which are often constrained to modeling the potential distribution of one biological unit (e.g. lineage or species) at a time. By comparing SDM performance for the whole species or where observation and predictions were partitioned among geographically discontinuous genetic lineages, we first identified the appropriate biological unit for modeling sea scallop. Prediction errors, in particular contiguous omissions at the northern range margins were effectively halved in genetic lineage SDM (Total error=15%) verses whole species SDM. Remaining SDM prediction error was strongly associated with: i) Sharp climatic gradients (abrupt and persistent spatial shifts in limiting temperatures) found within continental shelf breaks and bottom channels. ii) A biotic gradient in the predation of sea scallop juveniles by the sand star within the Hudson Shelf USA. Our findings highlight how the accuracy of marine SDM is dependent on capturing the appropriate biological unit for modeling (e.g. lineages rather than species) and adequately resolving limiting abiotic and biotic interaction gradients.

scholarly journals Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)

2021 ◽  
Vol 12 ◽  
Author(s):  
Veit Herklotz ◽  
Aleš Kovařík ◽  
Volker Wissemann ◽  
Jana Lunerová ◽  
Radka Vozárová ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Distance Matrix ◽  
Distance Measures ◽  
Data Sets ◽  
Neighbor Joining ◽  
Multivariate Statistical ◽  
The Family ◽  
Synthetic Hybrids ◽  
Evolutionary Lineages ◽  
Subfamilial Classification

Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a “repeatomic fingerprint,” and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.

scholarly journals Molecular Approach to the Identification and Phylogenetic Biogeography of Snail Telescopium telescopium Using mt-COI Gene Sequences

2018 ◽  
Author(s):  
Satheesh Kumar Palanisamy ◽  
Prasanna Kumar Chinnamani ◽  
Purushothaman Paramasivam ◽  
Umamaheswari Sundaresan
Keyword(s):  
Evolutionary Relationship ◽  
Molecular Data ◽  
Coi Gene ◽  
Data Sets ◽  
Geographical Variations ◽  
Group I ◽  
South West Coast ◽  
Limited Gene Flow ◽  
Coi Sequences ◽  
Mitochondrial Cytochrome Oxidase

We aimed to apply DNA barcoding tool for the molecular identification of horn snails T. telescopium using mitochondrial cytochrome oxidase I gene (mt-COI) and to investigate their evolutionary relationship along with location-specific bio-geographical variations. The molecular data sets of this study indicate that strong probability of T. telescopium species taxonomic confirmation using mt-COI sequences. Results of the phylogenetic analysis suggest that Telescopium sp. was monophyletic with disseminated nodes and the evolution of group II originated from group I. The substantial genetic distance among the mt-COI sequences (0.005 to 0.184) were noticed. Large divergence between the south-west coast of India and Australia region population indicates limited gene flow between the two continents. Our study suggests that the genera Telescopium is globally ubiquitous but genetically showing inter-region differentiation. We conclude that mt-COI gene can be used to identify gastropod T. telescopium species.

Shrimp farming with pen enclosures in south Brazil.

2020 ◽  
Author(s):  
Felipe Suplicy
Keyword(s):  
Coastal Lagoons ◽  
Low Cost ◽  
Shrimp Farming ◽  
Small Scale ◽  
Southern Brazil ◽  
Alternative Source ◽  
Patos Lagoon ◽  
Artificial Aeration ◽  
Water Pumping ◽  
By Products

Abstract Native shrimp farming has been considered as an important alternative source of income for artisanal fishers and farmers in the Patos Lagoon estuary, southern Brazil. Considering the potential of estuarine areas for shrimp farming, the application of a low-cost structure to culture shrimp such as a pen is being proposed to complement capture fisheries and agriculture. From an economic standpoint, the use of pens has several advantages over a traditional pond-based culture system as land, water pumping and artificial aeration devices are not required. Relatively inexpensive materials may be employed for pen construction and running costs are minimized by the use of by-products from capture fishing to feed shrimps. These factors represent important points in lowering costs, which may turn small-scale shrimp farming into an economically feasible activity. Although this activity is in its initial stages of development, there is a strong tendency for the spread of this practice in coastal lagoons and estuaries in southern Brazil.

scholarly journals Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis

2020 ◽  
Vol 27 (2) ◽  
pp. 427-433
Author(s):  
Mohammad Ajmal Ali ◽  
M Oliur Rahman ◽  
Joongku Lee ◽  
Fahad Al Hemaid ◽  
Sidanand V Kambhar ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Larrea Tridentata ◽  
Data Sets ◽  
Minimum Evolution ◽  
Likelihood Methods ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Plant Taxon ◽  
Systematic Relationships ◽  
Relationship Of

The systematic relationships of Krameriaceae have changed considerably. The phylotranscriptomic data sets provide highly informative data for resolving deeper‐level phylogenetic relationships. The phylotranscriptomic analyses to infer evolutionary relationships of Krameriaceae in the order Zygophyllales using the Minimum Evolution, Maximum Parsimony and Maximum Likelihood methods recovered similar topology and taxon proximity. Under the Zygophyllales clade, Krameria lanceolata Torr. of the family Krameriaceae nested with Tribulus eichlerianus K.L. Wilson and Larrea tridentata (Sessé & Moc. ex DC.) Coville belonging to the family Zygophyllaceae with strong nodal support. The phylotranscriptomic analyses suggest that the family Krameriaceae is sister to Zygophyllaceae. Bangladesh J. Plant Taxon. 27(2): 427-433, 2020 (December)

An example of spectrum imaging used for comparison of EELS quantitative analysis techniques on Al-Li

1991 ◽  
Vol 49 ◽  
pp. 726-727
Author(s):  
John A. Hunt
Keyword(s):  
Quantitative Analysis ◽  
Large Data ◽  
Difference Spectrum ◽  
Large Data Sets ◽  
Foil Thickness ◽  
Data Sets ◽  
Analysis Techniques ◽  
Spectrum Imaging ◽  
Normal Spectrum ◽  
Electron Energy Loss

Spectrum-imaging is a useful technique for comparing different processing methods on very large data sets which are identical for each method. This paper is concerned with comparing methods of electron energy-loss spectroscopy (EELS) quantitative analysis on the Al-Li system. The spectrum-image analyzed here was obtained from an Al-10at%Li foil aged to produce δ' precipitates that can span the foil thickness. Two 1024 channel EELS spectra offset in energy by 1 eV were recorded and stored at each pixel in the 80x80 spectrum-image (25 Mbytes). An energy range of 39-89eV (20 channels/eV) are represented. During processing the spectra are either subtracted to create an artifact corrected difference spectrum, or the energy offset is numerically removed and the spectra are added to create a normal spectrum. The spectrum-images are processed into 2D floating-point images using methods and software described in [1].

Computer-aided methods for 3-D visualization of serial sections and thick biological specimens

1992 ◽  
Vol 50 (2) ◽  
pp. 1060-1061
Author(s):  
Mark Ellisman ◽  
Maryann Martone ◽  
Gabriel Soto ◽  
Eleizer Masliah ◽  
David Hessler ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Three Dimensional ◽  
Neuritic Plaque ◽  
Dimensional Structure ◽  
Data Sets ◽  
Molecular Physiology ◽  
Research Activities ◽  
Computer Aided ◽  
Dimensional Reconstruction

Structurally-oriented biologists examine cells, tissues, organelles and macromolecules in order to gain insight into cellular and molecular physiology by relating structure to function. The understanding of these structures can be greatly enhanced by the use of techniques for the visualization and quantitative analysis of three-dimensional structure. Three projects from current research activities will be presented in order to illustrate both the present capabilities of computer aided techniques as well as their limitations and future possibilities.The first project concerns the three-dimensional reconstruction of the neuritic plaques found in the brains of patients with Alzheimer's disease. We have developed a software package “Synu” for investigation of 3D data sets which has been used in conjunction with laser confocal light microscopy to study the structure of the neuritic plaque. Tissue sections of autopsy samples from patients with Alzheimer's disease were double-labeled for tau, a cytoskeletal marker for abnormal neurites, and synaptophysin, a marker of presynaptic terminals.

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