scholarly journals Habitat conditions drive phylogenetic structure of dominant bacterial phyla of microbialite communities from different locations in Mexico

2016 ◽  
Vol 64 (3) ◽  
Author(s):  
Carla M. Centeno ◽  
Omar Mejía ◽  
Luisa I. Falcón
Keyword(s):  
Species Abundance ◽  
Genetic Data ◽  
Main Process ◽  
Phylogenetic Structure ◽  
Data Set ◽  
Bacterial Phyla ◽  
Hypervariable Regions ◽  
Complete Dataset ◽  
Random Events ◽  
Relatedness Analysis

Community structure and composition are dictated by evolutionary and ecological assembly processes which are manifested in signals of, species diversity, species abundance and species relatedness. Analysis of species coexisting relatedness, has received attention as a tool to identify the processes that influence the composition of a community within a particular habitat. In this study, we tested if microbialite genetic composition is dependent on random events versus biological/abiotical factors. This study was based on a large genetic data set of two hypervariable regions (V5 and V6) from previously generated barcoded 16S rRNA amplicons from nine microbialite communities distributed in Northeastern, Central and Southeastern Mexico collected in May and June of 2009. Genetic data of the most abundant phyla (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes, and Cyanobacteria) were investigated in order to state the phylogenetic structure of the complete communities as well as each phylum. For the complete dataset, Webb NTI index showed positive and significant values in the nine communities analysed, where values ranged from 31.5 in Pozas Azules I to 57.2 in Bacalar Pirate Channel; meanwhile, NRI index were positive and significant in six of the nine communities analysed with values ranging from 18.1 in Pozas Azules I to 45.1 in Río Mesquites. On the other hand, when comparing each individual phylum, NTI index were positive and significant in all groups, except in Cyanobacteria for which positive and significant values were only found in three localities; finally, NRI index was significant in only a few of the comparisons performed. The results suggest that habitat filtering is the main process that drives phylogenetic structure in bacterial communities associated to microbialites with the exception of Cyanobacteria where different lineages can contribute to microbialite formation and growth.

scholarly journals Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 78
Author(s):  
Orestis Nousias ◽  
Konstantinos Tzokas ◽  
Leonidas Papaharisis ◽  
Katerina Ekonomaki ◽  
Dimitrios Chatziplis ◽  
...  
Keyword(s):  
Genetic Data ◽  
Population Parameters ◽  
Genetic Population ◽  
Data Set ◽  
Overall Evaluation ◽  
Relatedness Analysis ◽  
Breeding Schemes ◽  
Established Population ◽  
Selection Of ◽  
Microsatellite Analyses

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.

Maintenance of a Genetic Data Set on Multiple Data Base and Statistical Analysis Systems

1982 ◽  
Vol 61 (s109) ◽  
pp. 34-34
Author(s):  
Samuel J. Agronow ◽  
Federico C. Mariona ◽  
Frederick C. Koppitch ◽  
Kazutoshi Mayeda
Keyword(s):  
Statistical Analysis ◽  
Data Base ◽  
Genetic Data ◽  
Data Set ◽  
Multiple Data

Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand

The Condor ◽  
2019 ◽  
Vol 121 (3) ◽  
Author(s):  
Nicolas J Rawlence ◽  
Matt J Rayner ◽  
Tim G Lovegrove ◽  
Debbie Stoddart ◽  
Melanie Vermeulen ◽  
...  
Keyword(s):  
New Zealand ◽  
Conservation Management ◽  
Species Conservation ◽  
Genetic Data ◽  
Mitochondrial Control Region ◽  
Phylogenetic Structure ◽  
Management Guidelines ◽  
Conservation Concern ◽  
Cryptic Biodiversity ◽  
Archival Dna

Abstract Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.

scholarly journals Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

2008 ◽  
Vol 74 (17) ◽  
pp. 5422-5428 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Noha H. Youssef ◽  
Anne M. Spain ◽  
Cody Sheik ◽  
Fares Z. Najar ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Tall Grass ◽  
Data Set ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Soil Bacterial ◽  
Close Relatives ◽  
Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

Burrow occupancy and productivity at coastal sooty shearwater (Puffinus griseus) breeding colonies, South Island, New Zealand: can mark - recapture be used to estimate burrowscope accuracy?

2003 ◽  
Vol 30 (4) ◽  
pp. 377 ◽  
Author(s):  
Chris Jones ◽  
Susan Bettany ◽  
Henrik Moller ◽  
David Fletcher ◽  
Justine de Cruz
Keyword(s):  
New Zealand ◽  
Survival Rates ◽  
Species Abundance ◽  
Adult Survival ◽  
Egg Survival ◽  
Global Pattern ◽  
Data Set ◽  
Mark Recapture ◽  
Mammalian Predators ◽  
Occupancy Rates

Breeding colonies of sooty shearwaters ('muttonbird', tïtï, Puffinus griseus) on mainland New Zealand have declined in recent years. New data on burrow occupancy and colony productivity for seven sooty shearwater breeding colonies on the coast of Otago, New Zealand for the 1996–97 and 1997–98 breeding seasons are presented and analysed as part of a five-year data set. Detection of a burrow's occupants using a fibre-optic burrowscope may underestimate absolute occupancy rates, but is still of value in the analysis of trends. Detection probabilities estimated by the novel use of mark–recapture models corresponded with those of previous studies of the technique's accuracy. Mainland declines are associated with a lack of control of introduced mammalian predators at most mainland colonies superimposed on a global pattern of decline in the species' abundance. Large numbers of recovered carcasses and an absence of burrow activity at two small mainland colonies show the decline to extinction of these colonies over the five years of collecting data. At one mainland colony with intensive predator control, survival rates and parameter variances are comparable with those found on a predator-free offshore island. All other mainland colonies showed negligible breeding success. There was a significant positive relationship between egg survival and an index of relative adult survival, with an apparent threshold below which few eggs hatch. Adult survival during the breeding season is likely to be the most important parameter in maintaining a colony's viability.

Variance heterogeneity, transformations, and models of species abundance: a cautionary tale

2004 ◽  
Vol 61 (7) ◽  
pp. 1294-1302 ◽  
Author(s):  
Brian H McArdle ◽  
Marti J Anderson
Keyword(s):  
Type I Error ◽  
Species Abundance ◽  
Ecological Systems ◽  
Type I ◽  
Data Set ◽  
Bootstrap Tests ◽  
Inflated Type ◽  
The Mean ◽  
Nonparametric Alternatives ◽  
Mean Variance

Ecological systems have intrinsic heterogeneity. Counts of abundances of species often show heterogeneity of variances among observational groups or populations. This is most often dealt with by using a transformation of the data followed by a traditional statistical analysis that requires homogeneity. Such an approach is extremely useful when the mean–variance relationship is consistent across the data set. In some situations, however, the mean–variance relationship does not stay constant, e.g., the degree of spatial aggregation of organisms can change in space and time. In these cases, transforming the data to "fix" the problem of heterogeneity can result in apparently grossly inflated type I error. The use of a transformation alters the model under test and also has an important effect on the spatial scale of the hypothesis. The use of nonparametric alternatives, such as permutation or bootstrap tests, does not solve this problem. Explicit models of these kinds of distributional changes, where they occur, are necessary.

scholarly journals EFFECTS OF THERMODYNAMICAL PROCESSES ON RADIOCESIUM BEHAVIOR IN LAKE TAPELIAI / TERMODINAMINIŲ PROCESŲ ĮTAKA RADIOCEZIO ELGSENAI TAPELIŲ EŽERE

2012 ◽  
Vol 3 (6) ◽  
pp. 95-100
Author(s):  
Anastasija Moisejenkova ◽  
Aloyzas Girgždys ◽  
Nikolaj Tarasiuk
Keyword(s):  
Lake Sediments ◽  
Water Column ◽  
Lake Water ◽  
Sediment Surface ◽  
Main Process ◽  
Complex Data ◽  
Data Set ◽  
Activity Concentrations ◽  
Lake Bottom ◽  
Integrated Study

The article presents the results of the integrated study of radiocesium behavior in Lake Tapeliai using not only conventional data on radiocesium activity concentrations in lake water and sediments but also a complex data set on seasonal variations and vertical profiles of standard water variables. Radiocesium activity concentrations in lake water as well as the vertical structure of the water column considerably depend on the inflows of the colored waters from the swampy watershed of the lake enriched in radiocesium. The global fallouts are mainly responsible for radiocesium inventory in lake sediments, which reaches maximum in the upper part of the water column above the ~5.4-m depth. The maximum values of radiocesium inventories in lake sediments are consistent with the respective densities of its deposits in the nearest forest soils. The main process of sediment activation is the direct sorption of radiocesium onto the sediment surface. Sedimentation rates in the lake vary mainly in the range of 3.5–5 mm·a–1. Lake bottom feeding sources located mainly on the southern terrace as well as their related near-bottom flows reduce respective sedimentation and radiocesium inventories in the sediments. Santrauka Straipsnyje nagrinėjama radiocezio elgsena Tapelių ežere, naudojant ne tik radiocezio savitojo ir tūrinio aktyvumų duomenis, bet ir standartinius vertikaliuosius parametrus, tokius kaip temperatūra, elektros laidumai ir oksiduoto sluoksnio storis. Radiocezio aktyvumas ežero vandenyje priklauso nuo spalvoto pelkinio vandens, kuriame yra radiocezio, patekimo į ežerą. Radiocezio apkrova dugno nuosėdose yra didžiausia viršutinėje ežero dalyje, t. y. iki 5,4 m gylio. Sedimentacijos greitis svyruoja 3,5–5 mm·m–1. Ežero priedugniniai vandens šaltiniai daugiausia išsidėstę pietinėje ežero terasoje, jų srovės sumažina sedimentaciją ir radiocezio apkrovą dugno nuosėdose.

When are leaves good thermometers? A new case for Leaf Margin Analysis

Paleobiology ◽  
1997 ◽  
Vol 23 (3) ◽  
pp. 373-390 ◽  
Author(s):  
Peter Wilf
Keyword(s):  
Species Richness ◽  
Multivariate Data ◽  
Species Abundance ◽  
Western Hemisphere ◽  
Mean Annual Temperature ◽  
Leaf Margin ◽  
Data Set ◽  
Leaf Analysis ◽  
Climate Analysis ◽  
Margin Analysis

Precise estimates of past temperatures are critical for understanding the evolution of organisms and the physical biosphere, and data from continental areas are an indispensable complement to the marine record of stable isotopes. Climate is considered to be a primary selective force on leaf morphology, and two widely used methods exist for estimating past mean annual temperatures from assemblages of fossil leaves. The first approach, Leaf Margin Analysis, is univariate, based on the positive correlation in modern forests between mean annual temperature and the proportion of species in a flora with untoothed leaf margins. The second approach, known as the Climate-Leaf Analysis Multivariate Program, is based on a modern data set that is multivariate. I argue here that the simpler, univariate approach will give paleotemperature estimates at least as precise as the multivariate method because (1) the temperature signal in the multivariate data set is dominated by the leaf-margin character; (2) the additional characters add minimal statistical precision and in practical use do not appear to improve the quality of the estimate; (3) the predictor samples in the univariate data set contain at least twice as many species as those in the multivariate data set; and (4) the presence of numerous sites in the multivariate data set that are both dry and extremely cold depresses temperature estimates for moist and nonfrigid paleofloras by about 2°C, unless the dry and cold sites are excluded from the predictor set.New data from Western Hemisphere forests are used to test the univariate and multivariate methods and to compare observed vs. predicted error distributions for temperature estimates as a function of species richness. Leaf Margin Analysis provides excellent estimates of mean annual temperature for nine floral samples. Estimated temperatures given by 16 floral subsamples are very close both to actual temperatures and to the estimates from the samples. Temperature estimates based on the multivariate data set for four of the subsamples were generally less accurate than the estimates from Leaf Margin Analysis. Leaf-margin data from 45 transect collections demonstrate that sampling of low-diversity floras at extremely local scales can result in biased leaf-margin percentages because species abundance patterns are uneven. For climate analysis, both modern and fossil floras should be sampled over an area sufficient to minimize this bias and to maximize recovered species richness within a given climate.

scholarly journals Comparing the performance of analytical techniques for genetic parentage of half-sib progeny arrays

2009 ◽  
Vol 91 (5) ◽  
pp. 313-325 ◽  
Author(s):  
DEAN A. CROSHAW ◽  
MAUREEN B. PETERS ◽  
TRAVIS C. GLENN
Keyword(s):  
South Carolina ◽  
Multiple Mating ◽  
Probability Model ◽  
Natural Populations ◽  
Multiple Paternity ◽  
Genetic Data ◽  
Bayesian Probability ◽  
Published Data ◽  
Data Set ◽  
Analytical Approaches

SummaryThe prevalence of female multiple mating in natural populations is important for many questions in mating system evolution. Several statistical techniques use genetic data to estimate the number of fathers that contribute gametes to broods, but they have not been widely compared to assess the magnitude of differences in their performance. With a combination of new data and reanalysis of previously published data, we compared five analytical approaches: (1) allele-counting, (2) parental reconstruction in GERUD, (3) a Bayesian probability model to estimate the frequency of multiple mating (FMM), (4) computer simulations based on population allele frequencies in HAPLOTYPES and (5) Bayesian parental reconstruction in PARENTAGE. The results show that choice of analysis technique can significantly affect estimates of sire number. Estimates from GERUD conformed exactly to results obtained from strict exclusion of potential sires in an experimental context. However, estimates yielded by HAPLOTYPES and PARENTAGE sometimes exceeded the numbers from GERUD by as much as 120 and 55%, respectively. We recommend GERUD over these other approaches for most purposes because of its accuracy and consistency in this analysis. Our novel genetic data set allowed us to investigate the extent and frequency of multiple paternity in a marbled salamander (Ambystoma opacum) population in South Carolina, USA. A. opacum contrasted with other salamander species by having relatively low levels of multiple paternity (only 31–54% compared with 71–96%). Although A. opacum had the lowest level of multiple paternity under all analytical approaches used here, the magnitude of differences among species varied.

Clues to the function of bacterial microcompartments from ancillary genes

2021 ◽  
Author(s):  
Henning Kirst ◽  
Cheryl A. Kerfeld
Keyword(s):  
Metabolic Pathways ◽  
Transmembrane Proteins ◽  
Transcriptional Regulators ◽  
Building Blocks ◽  
Data Set ◽  
Bacterial Phyla ◽  
Bacterial Microcompartments ◽  
Shell Proteins ◽  
Regulation Mechanisms ◽  
Protein Shell

Bacterial microcompartments (BMCs) are prokaryotic organelles. Their bounding membrane is a selectively permeable protein shell, encapsulating enzymes of specialized metabolic pathways. While the function of a BMC is dictated by the encapsulated enzymes which vary with the type of the BMC, the shell is formed by conserved protein building blocks. The genes necessary to form a BMC are typically organized in a locus; they encode the shell proteins, encapsulated enzymes as well as ancillary proteins that integrate the BMC function into the cell's metabolism. Among these are transcriptional regulators which usually found at the beginning or end of a locus, and transmembrane proteins that presumably function to conduct the BMC substrate into the cell. Here, we describe the types of transcriptional regulators and permeases found in association with BMC loci, using a recently collected data set of more than 7000 BMC loci distributed over 45 bacterial phyla, including newly discovered BMC loci. We summarize the known BMC regulation mechanisms, and highlight how much remains to be uncovered. We also show how analysis of these ancillary proteins can inform hypotheses about BMC function; by examining the ligand-binding domain of the regulator and the transporter, we propose that nucleotides are the likely substrate for an enigmatic uncharacterized BMC of unknown function.

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