bluuebunny/crossref_metadata_2025 huggingface dataset:
Acanthocephala
Authors: Richardson DJ
Published: April 2013

The phylum Acanthocephala is comprised of more than 1000 species of pseudoceolomic helminths, which, as adults, occur exclusively in the vertebrate small intestine. The most commonly parasitised definitive hosts are bony fishes, followed by birds, mammals and rarely amphibians and reptiles. Acanthocephalans are characterised by the possession of a head called a proboscis bearing hooks and spines that enable them to attach to the intestinal wall of their definitive host. Acanthocephalans are dioecious and exhibit sexual dimorphism. As an adaptation to parasitism, acanthocephalans have secondarily lost their digestive system and acquire their nutrients by direct absorption across the body wall. Acanthocephalans are primarily osmoconformers, and respiration and excretion occur primarily by diffusion across the body wall. All acanthocephalans exhibit an indirect life cycle utilising an arthropod intermediate host. Despite their sometimes large size, acanthocephalans cause relatively little pathology. Although very rare, human infection does occur. Molecular evidence suggests that Acanthocephalans are phylogenetically most closely aligned with the rotifers.

Key Concepts:

As adults, acanthocephalans are parasites of vertebrates.

Acanthocephalans have secondarily lost their digestive system as an adaptation to parasitism.

Acanthocephalans are closely related to the rotifers.

Approximately 1200 species of acanthocephalans have been described.

Acanthocephalans get their name from the spiny head called a proboscis.
Arthropoda (Arthropods)
Authors: Blackstone Neil W
Published: April 2013

The Arthropoda is a phylum of ecdysozoan animals in which the epidermis produces a segmented, jointed and hardened exoskeleton, which has internal musculature. Each segment primitively bears a pair of jointed limbs. Limbs may be uniramous (one branched) or biramous (two branched). Segments tend to be grouped into body regions or tagmata. Each major group of arthropods is characterised by a particular tagmosis. Arthropods include groups that are wholly marine (the extinct trilobites); marine, terrestrial and freshwater (chelicerates and crustaceans); terrestrial and freshwater (insects) or exclusively terrestrial (myriapods). Arthropods exhibit unparalleled diversity and abundance along with a correspondingly large ecological impact. Recent phylogenomic studies are beginning to resolve arthropod relationships. Two of the largest groups of arthropods – crustaceans and insects – form a single clade, the Pancrustacea. A group containing remipede crustaceans is sister to insects. The Mandibulata (Pancrustacea and Myriapoda) is well supported, and the Oligostraca exhibit a sister‐group relationship to all other pancrustaceans.

Key Concepts:

Arthropods are characterised by a segmented, jointed and hardened exoskeleton that has internal musculature.

Major groups of arthropods exhibit a characteristic tagmosis.

Arthropods include trilobites, chelicerates, crustaceans, insects and myriapods.

Many arthropods have compound eyes.

Arthropod limbs may be uniramous (one branched) or biramous (two branched).

Arthropods include the only invertebrate group to evolve flight.

Arthropods are both extremely diverse and highly abundant.

The Pancrustacea includes the crustaceans and insects.

A group containing remipede crustaceans exhibits a sister‐group relationship to insects.

The Mandibulata includes the pancrustaceans and myriapods.
Crustacea (Crustaceans)
Authors: Blackstone Neil W
Published: April 2013

The Crustacea is a subphylum of arthropods defined by the nauplius larva, two pairs of antennae and biramous (‘two branched’) second antennae. Other limbs are biramous as well, and the body includes an abdomen, a thorax and a five‐segmented head. Mandibles and other specialised feeding appendages are present. The gut is lined with a cuticle that is molted along with the exoskeleton. A haemocoel and a dorsal, ostiate heart are present. Nephridial excretory organs may be specialised as antennal or maxillary glands. Crustaceans exhibit an incredible diversity and abundance, ranging from tiny planktonic or interstitial forms less than a millimetre in length to much larger forms, including shrimp, lobsters and crabs. An abundant fossil record is found, extending back to the Burgess Shale. Crustacean phylogeny has recently been roiled by the ‘pancrustacean hypothesis’: insects and crustaceans form one large clade. As traditionally viewed, crustaceans are thus very likely paraphyletic.

Key Concepts:

Crustaceans share several derived features: the nauplius larva, two pairs of antennae and biramous (‘two branched’) second antennae.

Crustaceans exhibit an abdomen, a thorax and a five‐segmented head.

Crustaceans have mandibles and other specialised feeding appendages.

Molting is necessary for crustacean growth and includes the cuticle‐lined gut.

Excretory organs may be specialised as antennal or maxillary glands.

Crustaceans exhibit an incredible diversity and abundance.

Crustaceans range from tiny planktonic or interstitial forms less than a millimetre in length to much larger and often commercially valuable forms such as shrimp, lobsters and crabs.

The crustacean fossil record extends back to the Burgess Shale.

Crustaceans and insects form one large clade, the pancrustaceans.

As traditionally viewed, crustaceans are paraphyletic.
Onychophora (Velvet Worms)
Authors: Wright Jonathan C
Published: April 2013

The phylum Onychophora, also known as ‘peripatus’, ‘velvet worms’ or ‘walking worms’, comprises over 180 described species. Onychophorans are exclusively terrestrial, but are susceptible to desiccation and are restricted to humid microsites. The majority of species inhabit tropical forest litter. Their flexible trunk, retractile limbs and ability to squeeze through small interstices all make them excellently adapted for life in decomposing wood and leaf litter. The head appendages are modified for form sensory antennae, slicing mandibles and slime papillae. The last are a unique trait of onychophorans and eject a rapidly polymerising glue, which is used to entangle their animal prey. Both morphological and molecular phylogenetic studies place the Onychophora at the base of the phylum Arthropoda. Gas exchange via an invaginated tracheal system and water‐conserving uricotely represent show convergent evolution with similar terrestrial adaptations in insects.

Key Concepts:

Onychophorans possess typical arthropod traits: a chitinous cuticle, metameric segmentation with paired segmental limbs and periodic moulting regulated by steroid ecdysones.

Gas exchange in onychophorans is accomplished by spiracles scattered over the body surface and which open into fan‐like clusters of tracheal tubules.

The flexible trunk functions as a hydrostatic skeleton, deformed by antagonising circular and longitudinal muscle layers beneath the integument.

Onychophorans possess little resistance to desiccation and are mostly confined to humid habitats in the tropics and sub‐tropics.

Some species are able to take up water by eversible coxal vesicles at the leg‐bases.

The anterior limbs are specialised as sensory antennae, slicing mandibles and slime papillae that eject a fast‐polymerising glue to entangle prey.

Most onychophorans possess separate sexes (gonochoristic) and fertilisation involves various mechanisms of spermatophore transfer, often during an elaborate courtship.
Tardigrada
Authors: Wright Jonathan C
Published: April 2013

The Tardigrada comprise a phylum of over 1070 described species of minute aquatic animals. The metamerically segmented trunk possesses four pairs of squat, lobopodial limbs with terminating claws; the claw morphology is taxonomically important. Tardigrades are fluid feeders, piercing animal or plant cells with eversible stylets and ingesting fluid with a muscular, pumping pharynx. Two classes are recognised: the Heterotardigrada and Eutardigrada and heterotardigrades include the majority of marine genera. Most tardigrades, however, inhabit interstitial or temporary water bodies in soil, mosses and lichens, surviving periods of drying by cryptobiosis. During this process, animals may sustain a complete loss of ‘free’ liquid water and accompanying cessation of metabolism. In this dehydrated state, tardigrades display suspended senescence and remarkable resistance to environmental extremes. The phylogenetic status of tardigrades has long been contentious, but recent molecular analyses show that tardigrades are basal arthropods and should be reclassified accordingly.

Key Concepts:

Tardigrades, also known as water bears, are minute lobopodial arthropods occurring worldwide from Arctic to tropical latitudes.

All tardigrades are aquatic; they are particularly associated with interstitial water of mosses, lichens and soils.

Two classes are recognised: the Eutardigrada and the Heterotardigrada; the latter includes some marine species.

All tardigrades possess piercing stylets that are used to puncture the cells of plants or, in a few species, animal prey.

In many species of tardigrades, the eggs and adults are capable of surviving extreme dehydration and sub‐freezing temperatures by means of cryptobiosis.

Cryptobiotic organisms frequently accumulate disaccharides or polyols that may stabilise membranes and proteins and/or promote vitrification.

Cryptobiotic tardigrades may be ametabolic and show extreme longevity and high resistance to temperature, radiation and microgravity.

Recent molecular phylogenetic studies unite the Tardigrada and Eutardigrada as a natural group within the collective arthropod taxa (Panarthropoda).
Messel
Authors: Schaal Stephan
Published: April 2013

The Messel site, Germany, is a former maar with lake sediments including a laminated algal rock, the dark‐brown to black Messel oilshale. It became famous with the discovery of its extraordinarily well‐preserved fossils of Middle Eocene age, 47 mya. The spectrum of fossil specimen is unusually extensive and contains plants, insects, fishes, reptiles, amphibian, birds and mammalian fossils. Some insects are preserved with their structural colours and vertebrates can be found with complete and articulated skeletons and even with gut contents. Anaerobe bacteria trace hair, feathers and skin. Messel site enables a view to the evolution and radiation of mammals after the extinction of dinosaurs. The palaeoclimate for the Messel forest was proved by a flora which suggests an equable warm and humid climate with some seasonality. Messel site is unique for the lower Eocene and became United Nations Educational, Scientific and Cultural Organisation (UNESCO) World heritage site in the year 1995.

Key Concepts:

A natural catastrophe established the basis for the Messel maar; numerous water vapour explosions created a volcanic crater, where freshwater lake and oilshale developed.

Messel flora is interpreted as the remains of a warm and humid palaeoclimate with some seasonality.

Preservation of 7 pairs of turtles are the first records worldwide of fossilised copulating vertebrates.

The discovery of the oldest preserved anteater made it possible to reconstruct a connection to South America via Africa before the existence of the maar Messel.

Preservation of complete skeletons, including hair and feathers enable scientists to make statements to the individual strategies of vertebrate locomotion.

Gut contents in vertebrates and coprolites offer a unique opportunity to study feeding and food web.

Some insects like jewel beetles and leaf beetles are preserved with their structural colours, which give them an iridescent metallic hue.
Extinction
Authors: MacLeod Norman
Published: April 2013

Extinction 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

The 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

The 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

Most 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

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

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

In 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

Reinforcement 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

Chromosomal 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

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

Drift 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.
Coalescence: the Sharing of Ancestry of Alleles
Authors: Brookfield John FY
Published: April 2013

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

Industrial 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

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

The 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

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

Cyanogenesis 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.