bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coalescence: the Sharing of Ancestry of Alleles
Authors: Brookfield John FY 
Published: April 2013

Abstract

Coalescence is the process whereby alleles sampled from a population can be traced back to a single ancestor. When the variation that exists between the alleles is neutral in its effect on Darwinian fitness, the analysis of expected patterns in coalescent processes is simple, due to the independence of the phylogeny of the alleles from the mutational changes that they have undergone. The structure of this genealogy can reveal whether the population has been constant in size and whether it has been geographically subdivided. It can also suggest whether selection has operated, particularly if unexpected patterns are seen at individual genetic loci, and not genome‐wide. However, due to the intrinsically stochastic nature of the coalescent process, inference of demographic changes from a coalescent analysis is difficult, particularly when only one or a few loci are examined.

Key Concepts:

Allelic DNA sequences sampled from a population share common ancestry and are connected by a phylogeny.

If DNA sequence variation is neutral with respect to natural selection, and if the population has been panmictic and of constant size, the expected phylogenies of alleles are easy to predict.

The coalescent process predicts the expected level and distribution of DNA sequence variation in populations.

The expected level of variation is determined by the product of the neutral mutation rate and the effective population size.

If data from wild populations differ from the expectations of the coalescent process, possible explanations include population subdivision, changes in population size and the action of natural selection.

Recombination has the effect that the phylogenies of different genetic loci will be different, although they will be correlated if the loci are linked.

Although the demographic history of a population will influence the coalescent process and thus the variation in the alleles sampled from a population, the inherent stochasticity of the process makes it hard to infer demographic histories with confidence from genetic variation, especially if few loci are considered.
Industrial Melanism
Authors: Grant Bruce S 
Published: April 2013

AbstractIndustrial melanism refers to the evolution of dark body colours in animal species that live in habitats blackened by industrial soot. The phenomenon has been documented in numerous species that hide from predators by blending in with their backgrounds. Peppered moths provide one example. Before the industrial revolution, peppered moths in the UK were pale grey, but after their habitats became polluted with soot from coal‐fired industries, melanic (black) phenotypes became numerous and spread to other regions. Away from industrial centres, the pale phenotype remained common. Following clean air legislation a century later, the atmosphere improved, soot‐damaged habitats gradually recovered, and the pale phenotype returned as the predominant form. Parallel changes have occurred in America. The melanic and pale phenotypes are determined by genes, and the changes in their percentages in populations reflect natural selection. Experiments identify bird predation on the moth phenotypes as the agent of selection.Key Concepts:The natural colour patterns of animals are adaptations produced by natural selection.A change in frequency (percentage) of genetically determined phenotypes in natural populations is direct evidence of evolutionary change.Mutations introduce new genetic variation to a population, but recurrent mutations occur too rarely to bring about rapid changes in the frequency of genes.Random changes in the frequency of genes (genetic drift) are irregular and unpredictable in direction.Directional, rapid changes in the frequency of genetically determined phenotypes in populations result from natural selection.Historical records on phenotypic frequencies from population samples allow the assessment of natural selection.Gene flow (migration) retards genetic differentiation among geographically widespread populations.Clines indicate different selection pressures along environmental gradients; when selection is removed, migration homogenises the differences along a cline.Parallel evolution is ‘nature's replicate experiment’.
Molecular Evolution: Nearly Neutral Theory
Authors: Ohta Tomoko 
Published: April 2013

Abstract

Nearly neutral theory is an extension of the neutral theory and contends that the borderline mutations, whose effects lie between the selected and the neutral classes, are important at the molecular level. Under the strict neutral theory, the evolutionary rate is equal to the neutral mutation rate. Under the near‐neutrality, the situation is not so simple and the most significant difference between the neutral and the nearly neutral theories is that the latter predicts a negative correlation between evolutionary rate and species population size. The nearly neutral theory also predicts abundant rare alleles in the population as compared with strict neutrality. Genome‐wide data on protein evolution are mostly in accord with the nearly neutral theory. Genetic regulatory systems are highly complex. The near‐neutrality concept may be extended to the evolution of such systems, where epigenetics and robustness are important for gene expression and many mutations are weakly selected.

Key Concepts:

The emphasis of significance of weak selection in evolution distinguishes the nearly neutral theory from the neutral theory.

The nearly neutral theory contends that the interplay of drift and weak selection is important and predicts that evolution is more rapid in small populations than in large populations.

Many observed patterns of protein evolution by measuring synonymous and nonsynonymous divergences are in accord with the nearly neutral theory.

Observed molecular polymorphisms within a population often show abundance of rare alleles, in accord with the prediction of the nearly neutral theory.

Numerous complex systems work together in living cells such as those in chromatin modelling/remodelling and in various signalling pathways. Interplay of drift and weak selection is important for evolution of such complex systems.
Molecular Clock: Testing
Authors: Battistuzzi Fabia Ursula , Filipski Alan J , Kumar Sudhir 
Published: April 2013

AbstractThe molecular clock hypothesis originally rested on the assumption of rate constancy across lineages of a phylogeny, which would produce an approximately steady rate of accumulation ofdeoxyribonucleic acidor amino acid changes through time. This assumption has been questioned on the basis of increasingly large data sets, which have shown significant variability of rates in evolutionary lineages. To address this issue, tests have been developed to examine whether rates of molecular evolution vary significantly among taxonomic groups or phylogenetic lineages. Two major types of tests exist: those based on comparisons of genetic distances and those based on likelihood ratios. The first ones compare genetic distances between two species (or groups of species) relative to an outgroup; the latter ones compare maximum likelihood values for the same phylogeny calculated with and without the constant rate assumption. In those cases where the rate constancy assumption is violated, modern molecular clocks (relaxed clocks) are now being applied to implement the rate heterogeneity in the time estimation process.Key Concepts:The original formulation of the molecular clock hypothesis refers to the approximately steady rate of accumulation of DNA or amino acid changes through time.The assumption underlying the strict molecular clock is that evolutionary rates across lineages are constant.Molecular clock tests have been developed to assess the validity of the rate constancy assumption for DNA and amino acid sequences.Rate testing relies on a measure of genetic distance (branch length) for two or more lineages relative to an outgroup or on likelihood ratio tests.Distance‐based rate tests compare rates between two lineages or groups of lineages using the number of nucleotide or amino acid differences between them.Likelihood ratio tests use the chi‐square statistic to compare the likelihoods of a tree calculated with and without the rate constancy assumption.Unequal rates can be modelled by relaxed molecular clocks assuming two alternative models: ancestor and descendant lineages are autocorrelated or uncorrelated.Local rate testing using Bayes Factors is used to distinguish between autocorrelated and uncorrelated rate variation in Bayesian‐based relaxed clock methods.If evolutionary rates are heterogeneous among lineages, the violating lineages can be pruned from the data set or divergence times can be estimated with relaxed clock methods.Molecular clocks can be used to time divergences for which rare or incomplete palaeontological records exist.
Base Composition Patterns
Authors: Axelsson Erik , Webster Matthew T 
Published: April 2013

Abstract

Genomic GC content varies both between species and within individual genomes. The nature of this variation differs between groups of organisms. Bacteria exhibit little intragenomic variation in GC content, but a large range of variation between species. In contrast, higher eukaryotes exhibit a much narrower range of variation in GC content between species, but many have highly structured variation within their genomes, which may reflect a fundamental level of genome organisation. The causes of variation in GC content have been subject to debate, and it has been suggested that both natural selection and mutational biases may play a role. However, at least in vertebrates, much recent evidence points to a strong role of recombination in determining base composition patterns.

Key Concepts:

GC content shows considerable variation between species and within genomes.

GC content is rarely at equilibrium, and changes over evolutionary time.

Recent evidence points to a strong role of recombination in determining GC content.
Cyanogenesis in Higher Plants and Animals
Authors: Lechtenberg Matthias 
Published: April 2013

AbstractCyanogenesis describes the ability of living organisms to liberate hydrogen cyanide from stored cyanogenic glycosides, cyanogenic lipids or cyanohydrins on tissue damage by hydrolysis and/or decomposition. It has been described for over 2650 species of higher plants and some animals. Together with plant β‐glucosidases and hydroxynitrile lyases cyanogenic glycosides are the constituent part of a preformed defence system. Today it's generally accepted that cyanogenic glycosides also may serve as storage form for reduced nitrogen and sugar. Chemically, cyanogenic glycosides are glycosides of α‐hydroxynitriles (cyanohydrins). The structures are biogenetically related to only a few precursor amino acids. Biogenetically closely related are some noncyanogenic glucosides of β‐ and γ‐hydroxynitriles (cyanoglucosides). Their biological function is not fully understood until today. Many food plants are cyanogenic and great efforts are made to optimise detoxification. Humans are able to detoxify considerable amounts of HCN. Although acute intoxication is rare, the daily consumption of subacute amounts of cyanogenic glycosides leads to chronic diseases, caused by increased plasma levels of the human detoxification products. The presence of cyanogenic glycosides in the animal kingdom appears to be restricted to Arthropoda. Some insects, often aposematically coloured, eitherde novosynthesise cyanogenic glycosides and/or sequester them from their host plants.Key Concepts:Cyanogenic glycosides are secondary metabolites known from more than 2650 different plant species.Cyanogenic glycosides are glycosides of α‐hydroxynitriles, derived from five proteinogenic amino acids (Phe, Tyr, Val, Ile and Leu) and from the nonproteinogenic amino acid cyclopentenyl glycine. Acalyphin is apparently derived from nicotinic acid.Cyanogenic plants are able to liberate hydrogen cyanide from their cyanogenic glycosides upon disruption of plant tissue.Cyanogenic glycosides and their corresponding degrading enzymes (β‐glucosidases; hydroxynitrile lyases) are part of a preformed defence system. Thus, they can be regarded as phytoanticipins.Additional roles and functions of cyanogenic glycosides include storage of reduced nitrogen and sugar, transportation of nitrogen and the turnover of nitrogen into primary metabolism.The presence of cyanogenic glycosides in animals appears to be restricted to Arthropoda.Some insects are strongly associated with their cyanogenic host plants. They sequester the cyanogenic glycosides from these pants as well as carry outde novobiosynthesis of these compounds.
Sarcosporidiosis
Authors: Mehlhorn Heinz 
Published: April 2013

Abstract

Sarcosporidiosis is a disease that occurs worldwide in many animals and human beings as a result of oral infections with developmental stages of several
Sarcocystis
species, the life cycle of which includes two types of hosts: a prey and a predator. Humans may be involved in both groups. The prey hosts are herbi‐ or omnivores, which are infected by oral uptake of oocysts and sporocysts from the feces of the predator hosts, which are carnivorous beings including man. The specimens of the latter group are infected by eating raw or undercooked meat of the prey animals containing so‐called cyst merozoites (cystozoites) inside tissue cyst in muscle cells or in brain cells. The final hosts (=carnivores with the sexual development inside their intestinal cells) may suffer from diarrhoea in case of severe infections. The intermediate hosts (=prey hosts) may severely suffer from bleeding of inner blood vessels (where the schizonts and merozoites develop within the first month after infection) and by destruction of brain and muscle cells, where the cysts are formed. After about 3 months the cyst merozoites inside the tissue cysts are infectious for the final host.

Key Concepts:

Human intestinal infections with
Sarcocystis
species are completely prohibited by noneating raw or undercooked meat.

Strict separation of human, dog and cat feces from food of farm animals prohibits their infections with
Sarcocystis
species.

Sarcosporidiosis is completey avoidable on farms by strict hygienic measurements.

Deep freezing or cooking of meat will kill sarcosporidians.
Protozoan Pathogens: Identification
Authors: Walochnik Julia , Aspöck Horst 
Published: April 2013

Abstract

The identification of protozoan pathogens is based upon direct detection of the respective causative agent in clinical specimens and/or upon detection of specific immune reactions of the host. A considerable part of protozoan diagnostics still mainly relies on microscopy, however, in the past years molecular methods, particularly polymerase chain reaction (PCR)‐based techniques, have gained more and more importance. One of the big advantages of molecular techniques is that they usually allow identification below the genus level, which is often impossible by light microscopy. Serological tests are of great value in all tissue parasites and generally in most extra‐intestinal infections, whereas they only have limited importance in acute infections with short incubation times and in immunocompromised patients. Rapid card tests detecting parasite antigens and host antibodies are available for several important protozoan parasites and serve particularly well in the field setting.

Key Concepts:

Of the around 100 protozoan species that can infect humans, some are of prime importance for human health, including the causative agents of
malaria, amebiasis, leishmaniasis
and
sleeping sickness
.

Several protozoan infections show a more severe progression in the
immunocompromised host
, important examples are toxoplasmosis, pneumocystosis, cryptosporidiosis and visceral leishmaniasis.

The size of protozoan pathogens varies from
∼2 μm
(amastigote
Leishmania
spp.) to
∼150 μm
(

Balantidium coli

).

As parasite density in stool or body fluids may not be constant, the collection of repeated samples is often essential.

Proper collection, storage and transport of clinical specimens are of crucial importance for reliable laboratory diagnostics.

Accurate diagnosis includes both parasite
detection
and species (in some cases: genotype/serotype)
identification
.

Although numerous protocols for molecular detection of protozoan pathogens have been established in the past years, consent on the most reliable technique is missing for most protozoan taxa, thus demonstration of the causative agent in native material or stained smears is still the
gold standard
for detection.

Good
microscopic expertise
is essential: low parasite density and/or morphologic variability can result in false negative results, pseudo‐parasites and artefacts are common causes of false positive results.

In many protozoan taxa, morphology alone does not provide enough information for identification on or below the species level, this is today mainly based on
molecular biological methods
.
Euglena
Authors: Buetow Dennis E 
Published: April 2013

Abstract

Euglena

is a genus of single‐celled, free‐living microorganisms that show both plant‐ and animal‐like characteristics. Members of the genus are found widely in nature and mainly in fresh waters. Most are aerobic and use photosynthesis or many organic compounds as interchangeable sources of carbon and energy. The most studied species is the easily grown

E. gracilis

which, in spite of its relatively rigid surface, can be subfractionated to yield nuclei, mitochondria, chloroplasts, flagella and pellicles. Subfractions show some unusual characteristics: The nuclear envelope remains intact throughout mitosis and chromosomes are permanently condensed at all phases of the cell cycle, the mitochondrial respiratory chain has two terminal oxidases, and chloroplasts have three membranes reflecting their endosymbiotic evolutionary history. Various

Euglena

and some of their constituent molecules are useful for environmental biomediation and potentially useful biomedically.

Key Concepts:

Euglena
is a genus of single‐celled, free living microorganisms that show both plant‐ and animal‐like characteristics.

More than 250
Euglena
species have been described, though the actual number is not known.

The majority of
Euglena
species are green due to the presence of chloroplasts containing chlorophylls
a
and
b
.

Members of the genus
Euglena
are found widely in nature, inhabiting freshwater pools, ponds and lakes.

Euglena
are able to use photosynthesis and heterotrophic oxidative assimilation as interchangeable and apparently equivalent sources of carbon and energy.

How to classify
Euglena
has been a long‐standing problem; the genus has been claimed as photosynthetic protozoa by zoologists and as algae by botanists.

Studies on the genus
Euglena
, and especially

E. gracilis

, have been significant for understanding the biochemistry and molecular biology of nuclei and subcellular organisms.
Ciliophora
Authors: Lynn Denis H 
Published: April 2013

Abstract

Ciliophora is the name for a phylum of protists commonly called the ciliates. Ciliates are the most complex of cells, having an elaborate cytoskeleton, cilia and two different kinds of nuclei. Free‐living ciliates can be found in almost any habitat that has water – in soils, hot springs and Antarctic sea ice. Symbiotic species live as commensals in sea urchins or as parasites of lobsters and fish. Ciliate life histories can have specialised forms for dispersal and for resisting desiccation. Their cell cortex is supported by a complex framework of basal bodies or kinetosomes, microtubules and microfilaments. The kinetosomes form the central unit in an organellar structure called the kinetid, which is important to understanding phylogenetic relationships among ciliates. The pattern of fibres and microtubules in the kinetid identifies a ciliate to a major clade, along with the sequences of genes. These two features together identify 12 major clades or classes of ciliates.

Key Concepts:

Ciliates are characterised by three main features: they exhibit nuclear dimorphism; undergo conjugation as a sexual process; and typically have cilia at some stage in their life cycle.

Ciliates are the ‘top’ predators in microbial food webs, and were likely the major predatory group before the evolution of animals.

Parasitic ciliates can cause morbidity and death of animals, and are becoming particularly important in aquaculture operations.

Ciliates can have complex life cycles, including macrostome or cannibalistic stages, swarmers or dispersal stages and cyst or desiccation‐resistant stages.

The kinetid, an organellar complex in the cell cortex, is composed of at least one kinetosome and its cilium associated with two microtubular ribbons and a striated kinetodesmal fibril, whose patterned arrangement identifies a ciliate to a particular major clade or class.

Ciliate macronuclei divide in two ways, which suggest that macronuclear division evolved independently twice in the phylum: heterotrich ciliates divide their macronucleus principally using extramacronuclear microtubules while intramacronucleate ciliates divide their macronucleus with intramacronuclear microtubules.

Ciliates are divided into two major clades or subphyla and 12 classes based on features of the kinetid and sequences of genes.
Haptophyta
Authors: Jordan Richard W 
Published: April 2013

AbstractThe haptophytes are a group of microalgae, mostly marine, usually phototrophic, that possess a unique organelle, the haptonema, situated close to the flagella. Species identification traditionally relies on the morphology of the unmineralised or mineralised scales, although some recent advances have been made using molecular genetics. A number of taxa form blooms, some of which are toxic to marine life. The haptophytes include the calcified scale‐producing coccolithophorids, whose ancestors are partly responsible for the vast chalk deposits found in northern Europe.Key Concepts:The haptophytes are a monophyletic group that possess a haptonema.Species identification is based almost entirely on scale morphology and the combination of scale types.Blooms can sometimes cover vast areas of the ocean, contributing significantly to the global carbon and sulphur cycles, and may be toxic.Species‐specific viruses may be involved in the termination of haptophyte blooms.The majority of the chalk and limestone deposits of the Mesozoic and Cenozoic eras were produced by continual coccolith accumulation in the sediments.