bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extinction
Authors: MacLeod Norman 
Published: April 2013

AbstractExtinction is the act or process of the dying‐out of a species or evolutionary lineage. It is one of the most common of all ecological/evolutionary processes and represents an inevitable corollary of evolution by natural selection. Information on extinction comes from many sources, including laboratory experiments, field studies and the fossil record. The causes of short‐term extinctions involving few species can, in principle, be well understood. The causes of long‐term extinction events, such as those preserved in the fossil record, remain controversial. Although the contemporary biodiversity crisis is often referred to as a ‘sixth (mass) extinction’, levels of documented losses over the last 400 years have been modest by geological standards. Nevertheless, historical extinction rates are well above palaeontological background rates and are predicted to increase substantially over the next 200 years. Whether the number of species losses over this interval will reach geological magnitudes remains uncertain.Key Concepts:Extinction is a common and perfectly natural process.The processes that lead to extinction operate at a variety of spatial, ecological and temporal scales.Extinctions can be studied in the laboratory, in the field (modern) and in the fossil record (ancient); however, the ability of researchers to determine extinction patterns accurate and evaluate causal models in detail decreased as the spatial and temporal scales along those spectrum increase and as the biology of the organisms in question grows less familiar.Extinction processes can also be studied via mathematical simulation models. In many (though not all) cases, there is good agreement between the predictions of these mathematical models and field observations.The fossil record of extinction events exhibits two compelling patterns: (1) a historical pattern of long periods of relatively modest (= background) extinction intensities over time, interspersed by short, nonperiodic intervals of elevated extinction intensity and (2) a secular decline in the magnitude of background extinction intensity from the mid‐Palaeozoic to the Recent.Lower‐level peaks in extinction intensity are probably due to the operation of single major or idiosyncratic combinations of moderate intensity process that foster long‐term environmental change (e.g. sea‐level change, continental glaciation, large igneous province volcanism and asteroid/comet impact).Higher‐level peaks in extinction intensity (= mass extinctions) are probably due to idiosyncratic combinations of major process that foster long‐term environmental change (e.g., sea‐level change, continental glaciation, large igneous province volcanism and asteroid/comet impact).Over the last 400 years, extinctions have occurred at a rate that is well above background rates as inferred from the fossil record, but well below the range of even moderate geological extinction events. Models of maximum extinction intensities predicted over the next 200 years are matters for concern, but fall well below the intensities achieved by geological mass extinction events.
Extinction: Late Devonian Mass Extinction
Authors: McGhee George R 
Published: April 2013

AbstractThe Late Devonian mass extinction, which occurred 374.5 Ma, is one of the ‘Big Five’ mass extinctions in Earth history. Suggested causes of the mass extinction include oceanic anoxia and global cooling. The severe loss of biodiversity that occurred during the crisis was global, affecting both marine and terrestrial ecosystems and animal and plant communities. Both low‐temperature stresses due to global cooling and oxygen deprivation due to anoxia have been implicated as kill mechanisms in the Late Devonian mass extinction, and it is possible that the severity of the mass extinction was due to both processes operating in concert. The ultimate trigger for these kill mechanisms is still under debate: oceanic anoxia may have been triggered by eutrophication and terrestrial anoxia by an atmospheric oxygen minimum during the Late Devonian. Postulated triggers of global cooling range from abrupt and catastrophic – the volcanic‐winter hypothesis versus the impact‐winter hypothesis – to long‐term and gradual carbon dioxide downdraw from the atmosphere due to biological and chemical weathering of terrestrial rocks.Key Concepts:Early lobe‐finned fishes and tetrapod (four‐limbed) vertebrates were severely impacted by the Late Devonian mass extinction.A severe loss in biodiversity and a ‘floral crisis’ in land plants were triggered by the Late Devonian mass extinction.The destruction of Devonian‐style reefs triggered a permanent change in global marine ecosystems.Both low‐temperature stress (hypothermia) and oxygen deprivation (hypoxia) are implicated in the Late Devonian mass extinction.Both catastrophic asteroidal impact and catastrophic mantle plume volcanism are debated as causes of the Late Devonian mass extinction.The precise cause of the Late Devonian mass extinction remains unproved.
Extinction: End‐Permian Mass Extinction
Authors: Clapham Matthew E 
Published: April 2013

AbstractThe end‐Permian mass extinction (252.3 Ma) was an abrupt and severe loss of diversity on land and in the oceans, the largest extinction of the Phanerozoic. Recent palaeontological, geochemical and modelling studies link the extinction with eruption of the Siberian Traps flood basalts, which would have caused global warming, ocean acidification and shallow‐marine anoxia. On land, global warming and aridification were mostly responsible for the vertebrate and plant extinction. Although almost no marine group emerged unscathed, selectivity favoured more active animals, whereas sessile and heavily calcified taxa such as corals and reef‐building sponges suffered heavily. The recovery interval was unusually long, likely because of continuing stress, and the extinction resulted in permanent shifts in marine ecosystem composition and structure, giving rise to the mollusc‐rich communities that still dominate today.Key Concepts:The end‐Permian mass extinction was a severe crisis for nearly every plant and animal group, on land and in the oceans.The extinction was abrupt, apparently synchronous on land and in the sea, with the majority of taxonomic losses occurring over a few tens of thousands of years, approximately 252.3 Ma.In the marine realm, more actively motile animal groups fared relatively better during the extinction.Although low‐oxygen waters were widespread and contributed to the marine extinction, the primary cause most likely was global warming and ocean acidification from CO2released by Siberia Traps flood basalt volcanism.The terrestrial extinction was also caused by global warming and, among plants, the resulting dry conditions.It took an unusually long time (5–7 million years) for most marine and terrestrial ecosystems to recover from the extinction, likely because of continuing intermittent stress.The extinction triggered permanent changes in the composition and structure of marine ecosystems, giving rise to mollusc‐dominated communities that remain dominant today.
Plant Vacuoles
Authors: Neuhaus Jean‐Marc , Martinoia Enrico 
Published: April 2013

AbstractMost plant cells contain one or several vacuoles, which may occupy up to 95% of the cellular space. The vacuoles often appear empty under a light microscope (hence their name), except when they contain pigments or precipitated substances. The vacuole is delimited from the cytosol by the vacuolar membrane, which is also called tonoplast. Vacuoles are compartments of the secretory pathway derived from the endoplasmic reticulum and the Golgi apparatus. Their function include the storage of ions, sugars, proteins and xenobiotics. They also participate in volume changes during growth and development, movements such as stomata opening and closing and the maintenance of internal turgor pressure for the mechanical stiffness of green tissues. Although most plant cells have a single central vacuole, some cells have two different vacuoles with different contents and functions. Vacuole biogenesis is a complicated process involving several intermediate compartments, vesicle trafficking and fusion.Key Concepts:The large central vacuole plays an important role in temporary storage of metabolites, thus allowing keeping the metabolite levels constant in the cytosol.Plant cells can harbour two different types of vacuoles with different contents and functions.Vacuoles are compartments of the secretory pathway and derive their membrane (tonoplast) and protein content from the ERviathe Golgi apparatus and pre‐vacuolar compartments. Some storage vacuoles may however derive directly from the ER.Toxic compounds are preferentially stored in the large central vacuole, since in this compartment they do not interfere with plant metabolism.
Plant Mitochondria
Authors: Rose Ray J , Sheahan Michael B 
Published: April 2013

Abstract

Plant mitochondria, like the mitochondria of most other eukaryotes, use an electron transport chain (ETC) to translocate protons and generate
adenosine triphosphate (ATP)
. The generation of ATP through mitochondrial respiration also produces reactive oxygen species (ROS). In excess, ROS can damage the cell, but they are also an important signal produced in response to varied stresses. In addition to the classical electron transport chain, plant mitochondria possess an alternative ETC that can limit proton translocation (ATP synthesis) and modulate mitochondrial ROS production. Because mitochondria depend on proteins encoded by both mitochondrial and nuclear genomes, a sophisticated two‐way communication between the two organelles exists to ensure correct mitochondrial biogenesis and function. A balance of fusion and fission controls the morphology and number of plant mitochondria and is important for functionality and inheritance of their multipartite genome – an important determinant of male fertility.

Key Concepts:

Plant mitochondria are frequently small (1–2 μm long) but are highly pleomorphic and undergo frequent fusion and fission events.

Plant mitochondria have a smooth outer membrane and a highly convoluted inner membrane housing an electron transport chain (ETC) that drives adenosine triphosphate (ATP) synthesis.

In mitochondria, the production of reactive oxygen species (ROS) is inextricably linked to the production of ATP through oxidative phosphorylation.

ROS can damage macromolecules, but are important stress signalling molecules.

The alternative oxidase is a major component of the alternative ETC and can modulate ROS and ATP production.

There are approximately 2000 proteins in plant mitochondria mainly encoded by the nuclear genome with a smaller contribution from the mitochondrial genome.

Mitochondria participate in the biosynthesis of a range of coenzymes and vitamins.

Photorespiration, necessitated by the oxygenase activity of the carbon dioxide fixing enzyme ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO), involves interactions between chloroplasts, mitochondria and peroxisomes.

The nucleus controls mitochondrial gene expression (anterograde control), yet mitochondria can also influence nuclear gene expression (retrograde control).

Disrupted plant mitochondrial function often causes cytoplasmic male sterility (CMS) by perturbing pollen development.
Plant Cell Walls
Authors: Ivakov Alexander , Persson Staffan 
Published: April 2013

Abstract

The cell wall is the outer coat that provides a tough protective casing of the plant cell. Decades of research efforts have contributed to our current understanding of cell wall structure and function. The cell wall is composed primarily of three major classes of polysaccharide: cellulose, hemicellulose and pectin, as well as structural proteins, and phenolic and aliphatic polymers. In addition to structural roles, the cell wall has a multitude of important functions in plants. For example, cell wall expansion and its regulation is the basis of cell and plant growth, the cell wall gives plant cells their characteristic shapes, and it is strongly involved in defence responses against pathogens and herbivores. Furthermore, recent studies indicate some novel and remarkable roles for the cell wall in sensing processes during pattern formation in plant development. This article provides a general summary of the current understanding of cell wall structure and function.

Key Concepts:

Plant cell walls are crucial for plant morphology and development.

The primary walls are generally deposited during cell growth, while secondary walls may re‐inforce the extracellular space after cells have ceased to grow.

Three main polysaccharide classes may be discerned; cellulose, hemicelluloses and pectins.

The polysaccharides form an intricate and crosslinked architecture.

Several classes of cell wall structural proteins may be involved in scaffolding the deposition of cell wall material.

Enzymatic cell wall proteins are involved in modifying the properties of the cell wall during and after its assembly.

Cell wall modifications are a major regulatory mechanism of cell and plant growth.

The dynamic adjustment of cell wall properties is a crucial part of plant defence responses against pathogens and herbivores and mechanical injury.

Stress gradients in the cell wall are sensed by cells and may be a source of positional information during morphogenesis.
Plant Cell Division and its Unique Features
Authors: Cyr Richard J , Fisher Deb 
Published: April 2013

AbstractIn plant cells, mitosis involves many of the same ancestral components found in other eukaryotic cells, and the fundamental mitotic stages are similarly conserved. However, during the 1600 million years since plants and animals last shared a common ancestor, evolution has resulted in the appearance of unique (derived) features that reflect the evolutionary trajectory of plants. Unlike animal cells, plant cells are constrained by a cellulosic wall that largely precludes cell migration during overall development of the plant. Not only is cell migration limited by the wall, but this rigid matrix affects the character of the cytokinetic apparatus, which functions in a centrifugally expanding manner, rather than in a centripetally furrowing fashion. Another unique feature of plant cytokinesis involves the early determination (in G2) of the placement of the new cell plate, which has a long‐lasting impact on plants cells, tissues and organs in the developing plant.Key Concepts:The formation of the bipolar spindle involves multiple pathways.Although plant cell division has several derived features, plants make use of a highly conserved set of tools that are used by all eukaryotes during cell division.The preprophase band is a mitotic structure unique to plants (and some green algae) that functions in the formation of the prophase spindle and presages the location of the future cell plate at cytokinesis.Flowering plants lack centrioles and focused microtubule organising centres, but nonetheless, a bipolar spindle is assembled in most plant cells at prophase.Cytokinesis involves the construction of a new cell plate that is constructed in a centrifugal fashion by the phragmoplast (which arises from the remnants of the anaphase spindle).
Reinforcement
Authors: Sætre Glenn‐Peter 
Published: April 2013

AbstractReinforcement is the process, in which traits that increase pre‐zygotic isolation between two differentiated populations are favoured due to natural selection against the production of unfit hybrids or otherwise maladaptive interbreeding. It is a central process in many models of speciation and it is the only known process in which natural selection acts directly to promote speciation. Reinforcement was for long considered a controversial idea despite the fact that early theoretical models showed that the process could work under apparently realistic biological assumptions. Clarification of concepts along with the publications of refined theoretical models as well as convincing comparative and empirical case studies has more or less resolved the controversy; reinforcement works, but it is still debated how important it is in speciation.Key Concepts:Reinforcement is an increase in pre‐zygotic isolation between differentiated taxa caused by natural selection against maladaptive hybridisation.Reinforcement may contribute to speciation in previously geographically isolated taxa that experience secondary contact as well as to parapatric and sympatric modes of speciation.Reinforcement can lead to a sympatric divergence (character displacement) in any trait that reduces the likelihood of mating or fertilisation between diverging taxa, including secondary sexual traits, mating behaviour and traits affecting enzymatic communication between egg and sperm.Population genetic models show that assortative mating can increase as a response to genetic incompatibilities at other loci, but the process is sensitive to recombination.Factors that reduce recombination, including strong assortative mating, strong incompatibility selection and physical linkage promotes speciation by reinforcement.Comparative evidence suggests that pre‐zygotic isolation is stronger in sympatric species pairs than in allopatric ones, consistent with reinforcement.In well‐documented empirical cases of reinforcement genetic factors that reduce recombination has been identified and incompatibility selection tends to be strong.
Speciation: Chromosomal Mechanisms
Authors: Nevo Eviatar 
Published: April 2013

AbstractChromosomal speciation is one of the major modes of the origin of new species through the splitting of preexisting species. New species may originate by gene speciation, and also by the establishment of post‐mating reproductive isolation through structural chromosome rearrangements. The latter may induce low‐hybrid fitness, generated by macromutations, and even by micromutations, that is, molecular changes causing meiotic disturbances (e.g. GC incompatibilities), although the latter awaits empirical support. Criticism against the traditional model of chromosomal speciation led to renewed theoretical models arguing that chromosomal rearrangements can generate reproductive isolation between species by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to reproductive isolation and adaptive divergence and radiation. Likewise, coding and noncoding genomes, and novel chromosomal breakpoint regions can generate novel combinations of genes and regulatory elements that contribute to both adaptive radiation and ecological speciation. Chromosomal speciation is certainly an important speciation mode across life, although we cannot yet quantify it in relation to other modes. The spalacid example of blind subterranean mole rats in the East Mediterranean is presented as a widely studied case of chromosomal ecological speciation. The proportion of chromosomal speciation in nature, particularly in animals, remains a future challenge.Key Concepts:Speciation – the evolutionary process leading to the multiplication of species and generating biodiversity.Chromosomal speciation – the theory asserting that chromosomal rearrangements cause reproductive isolation between populations and lead to speciation.Peripatric speciation – the origin of a new species by budding from a parental species established beyond the periphery of the parental species range.Sympatric speciation – speciation without geographic (spatial) isolation; the origin of a new species within a deme.Polyploidy – the condition in which the number of chromosomes is an integral greater than two of the haploid numbers.Biological species concept (BSC) – defines species as groups of interbreeding natural populations that are reproductively (genetically) isolated from other such groups.Allopatric speciation – the evolution of a population into a separate species involving a period of geographic isolation.The evolutionary divergence of a single phyletic line into different niches or adaptive zones.
Macroevolution: Overview
Authors: Levinton Jeffrey S 
Published: April 2013

Abstract

Macroevolution is the sum of a range of processes that explain evolutionary changes that resulted in the diversity of major body plans of living organisms through geological time and at present. The field addresses the origin of major taxonomic groupings, the causes of evolutionary radiations, major biogeographic patterns and large‐scale extinctions. A diversity of approaches are required, including a firm understanding of the evolutionary relationships of the major branches of life, a geological context including good estimates of time and environment, accurate estimates of biological diversity through time and space, a complete study of the genetic and developmental mechanisms and processes that lead to the diversity of form of life, and an understanding of major episodes of origin and extinction in the history of life. Studies of genetic and developmental function have revealed the pattern and order of determination of form and the genetic variation that may matter in major evolutionary transitions. Our continuing refinement of the geological record has demonstrated coordinated origins or evolutionary radiations and mass extinctions. Characterisation of ancient climate, atmospheric and oceanic conditions, and palaeogeography have led to a better understanding of the likely mechanisms causing mass extinctions and to a lesser extent evolutionary radiations.

Key Concepts:

New approaches using genomic and DNA sequencing tools have produced much more accurate evolutionary trees that give us a context to explain the mechanisms of evolutionary transition.

The understanding of the cellular and genetic expression mechanisms of development has given us a large‐scale context to identify evolutionary transitions.

Form variation among major groups has to be understood in terms of evolutionary history, major adaptive constraints on form and to some extent by constraints on form that arise from limited variation of developmental mechanisms. The power of natural selection has been verified even with this larger‐scale approach.

Palaeontologists have devoted a great deal of effort to understanding whether speciation is an important component of evolutionary change and in sampling fossil populations at a finer scale.

On the larger scale, the fossil record shows strong fluctuations in diversity over time, but is especially organised by major coordinated evolutionary radiations and a few mass extinctions.
Drift: Theoretical Aspects
Authors: Ohta Tomoko 
Published: April 2013

AbstractDrift is the process by which gene frequency changes erratically in a population. Random sampling of gametes at reproduction is the main cause of drift, and therefore the population size of a species is most important, that is often measured by the effective size. Homozygosity and inbreeding may increase by drift. The significance of drift has become clear in studies of population genetics and evolution at the molecular level by the expansion of genome data. The effects of drift are estimated by statistical analyses of molecular data on polymorphisms and divergence among related species. In particular, the interplay of drift and selection is most important in understanding the evolution of interaction systems at various levels. Epigenetic mechanisms have significant influences on the interplay. Drift, selection, environmental factors, and epigenetics are thought to work together here.Key Concepts:Random sampling of gametes at reproduction is the major cause of drift in a finite population.Interplay of drift and selection is essential for evolution of complex systems, and the two become inseparable.Robust genetic systems enhance the effects of drift.Epigenetics gives opportunities for drift and selection to respond to environmental changes.