bluuebunny/crossref_metadata_2025 huggingface dataset:
Erythrocytes
Authors: Migliaccio Anna Rita F , Whitsett Carolyn
Published: April 2013

The erythrocyte is a highly specialized cell present in the blood designed for the transport of oxygen from the lungs to the body tissues and for the removal and transport of carbon dioxide from the tissues to the lungs. In primates, erythrocytes also clear the blood of complement‐bearing immune complexes and pathogens and exert anti‐inflammatory functions. The blood of an average adult contains approximately 25 million millions of erythrocytes. Maintaining this number of cells constant over time is a major challenge and requires production of as many as 210 billions of new erythrocytes per day (i.e. 24 millions per second). This production is tightly regulated by microenvironmental cues (growth factors) and by proteins present inside the cells (transcription factors). This regulation ensures that erythrocyte production is appropriately increased in response to sudden blood loss.

Key Concepts:

Erythrocytes are blood cells responsible for oxygen delivery to all the tissues of the body.

Erythrocytes are produced by hematopoietic stem cells present in the bone marrow.

Before birth, erythrocytes are derived from stem cell populations present in the yolk sac of the embryo and in the liver of the fetus.

Erythropoietin, a cytokine produced by the kidney, is primarily responsible for the regulation of erythrocyte production.

The bone marrow also contains several cytokines, which positively or negatively regulate erythrocyte production.

Erythrocytes exert their function by expressing on their surface and in their cytoplasm a number of erythroid‐specific proteins.

A series of DNA‐binding proteins (the erythroid transcription factors) assure that erythrocytes express adequate amounts of functional proteins.

The erythrocyte membrane is plastic and resistant to shear stress allowing the cells to pass through the microvasculature to deliver oxygen. The oxygen delivery function of the erythrocyte is performed by haemoglobin, a cytoplasmic protein whose structure is suited for oxygen transport/exchange.

The flexibility/deformability of the erythrocyte membrane is assured by a network between the proteins embedded in its lipid bilayer and the cell cytoskeleton.

Blood group antigens are epitopes present on the tertiary (glycosyl residues) or primary (amino‐acid sequence) structure of proteins present on the erythrocyte membrane.
Superantigens
Authors: Langley Ries J , Renno Toufic
Published: April 2013

Superantigens (SAgs) are microbial products that have the ability to promote massive activation of immune cells, leading to the release of inflammatory mediators that can ultimately result in hypotension, shock, organ failure and death. They achieve this by simultaneously binding and activating major histocompatibility complex class II molecules on antigen‐presenting cells and T‐cell receptors on T lymphocytes bearing susceptible Vβ regions. Why SAgs function in this manner is still not fully understood although it is thought that the resulting Th1 response may divert the immune system from effective microbial clearance and/or result in the cytokine‐mediated suppression and deletion of activated T cells. Many bacterial and viral species have adapted unrelated SAgs and this article will highlight some of the features of this diverse group of molecules, from the ways in which they interact with the host to the association of various SAgs with acute and chronic diseases.

Key Concepts:

Superantigens are toxins produced by many pathogenic bacteria and viruses.

Superantigens are defined as molecules that bind to the major histocompatibility complex (MHC) class II and active T cells bearing a particular T‐cell receptor beta chain variable (Vβ) domain.

Superantigens are implicated in inducing autoimmunity through the activation of autoreactive T cells that express particular Vβ elements.

Superantigens are responsible for staphylococcal and streptococcal toxic shock.

The superantigens ofStaphylococcus aureusare responsible for staphylococcal food poisoning.

The endogenous superantigen of the mouse mammary tumour virus (MMTV) causes deletion of T cells bearing a particular Vβ element, amplification of infected B cells and transmission of virus to the offspring.
Bacterial Chemotaxis
Authors: Eisenbach Michael
Published: April 2013

Bacteria can move by a variety of means, the most common one by rotating their flagella. This movement is often directed towards favourable chemicals (chemoattractants) or away from unfavourable chemicals (chemorepellents), a process termed chemotaxis. This modulation of swimming direction is the outcome of controlled changes in the direction of flagellar rotation. Therefore, mechanistically, the essence of bacterial chemotaxis is to control the direction of flagellar rotation. This control is done by a sophisticated signal transduction system, involving a small protein, CheY, which shuttles back and forth between the receptor complexes clustered at the pole of the cell and the flagellar motor complexes around the cell. These interactions are modulated by phosphorylation and acetylation. The excitatory signalling process involves amplification. The adaptation signalling involves methylation of the receptors. Even though bacterial chemotaxis is considered the best understood signalling system at the molecular level, many major questions are still waiting to be resolved.

Key Concepts:

In bacteria, chemotaxis is the motile response to stimuli and it serves as a means of cell–environment and cell‐to‐cell communication.

Bacteria sense stimulant gradients (chemoattractants and chemorepellents) temporally rather than spatially.

The chemotaxis‐specific receptors are clustered at the bacterial poles. This clustering is essential for signalling and amplification.

Bacteria swim by rotating their flagella. The direction of rotation determines the swimming mode. Therefore, the essence of bacterial chemotaxis is to control the direction of flagellar rotation.

The direction of flagellar rotation is modulated by the signalling molecule, CheY, according to changes in receptor occupancy.

CheY function is modulated by phosphorylation at both the excitatory and adaptation signalling phases. The latter also involves receptor carboxy methylation.

Phosphorylated CheY binds to the switch at the base of the flagellar motor and, thereby, changes the direction of rotation.
Adhesive Specificity and the Evolution of Multicellularity
Authors: Vleminckx Kris
Published: April 2013

Most of the cells in a multicellular organism are connected to each other and/or attached to a substrate. Physically this is mediated by adhesion molecules exposed on the cell surface and attached to the cell membrane either by covalent linkage to the lipid bilayer or by a membrane‐spanning region. The establishment of cell–cell interactions is a key aspect in the origin of multicellular life forms and the acquisition of tissue and organ organisation in metazoa. Adhesion is mediated by specific adhesion molecules belonging to the immunoglobulin superfamily, the cadherins, the integrins, the lectins and the proteoglycans. Adhesive associations by these molecules are organising forces in the embryo, controlling morphogenesis, tissue formation and organogenesis. In the adult, cell adhesion helps to control tissue homoeostasis, the organisation of the stem cell niche and the functioning of the immune system.

Key Concepts:

Multicellularity requires cell–cell adhesion molecules.

Cell adhesion molecules interact structurally and/or functionally with the cytoskeleton of the cell.

Cell adhesion molecules integrate extracellular and intracellular cues with intracellular signalling.

Cell adhesion molecules are more than molecular glue; they can act as signalling receptors inducing changes in the cytoskeleton and in gene expression.

Expression of cell adhesion molecules is under tight developmental control.

Changes in cell adhesion are a driving force for morphogenesis, tissue formation and organogenesis.

In the adult cell adhesion helps to maintain the stem cell niche and controls homeostasis.

Cell adhesion is essential for the functioning of the immune system.

Aberrant regulation of cell adhesion is involved in several human diseases.
Shikimate Pathway and Aromatic Amino Acid Biosynthesis
Authors: Tzin Vered , Galili Gad , Aharoni Asaph
Published: April 2013

The shikimate pathway consists of seven enzymatic reactions whose end product chorismate is the precursor for the synthesis of the aromatic amino acids Phe, Tyr and Trp. In fungi and plants, chorismate is a precursor for many specialised metabolites (i.e. secondary metabolites) that play an important role in the plant's interaction with its environment. The shikimate pathway and aromatic amino acid biosynthesis have been extensively studied in a variety of microorganisms, fungi and plants. Furthermore, the dual involvement of the shikimate and aromatic amino acid biosynthesis pathways in central and specialised metabolism still raises major questions regarding the genes and enzymes involved, and their control, their evolutionary origins and coordinated regulation with genes of associated pathways in response to altered environmental conditions and diverse developmental programs.

Key Concepts:

The shikimate pathway is the only known pathway for biosynthesis of chorismate and the aromatic amino acids Phe, Tyr and Trp.

The shikimate pathway is a bridge between central metabolism and specialised metabolism.

The shikimate pathway occurs in various groups of microorganisms, plants and parasites, whereas it does not occur in animals.

The pathway enzymes are being targeted for antimicrobial drug and herbicide design.

Shikimic acid is an essential metabolite that may balance the metabolic status of the pathway.

Chorismate is a branch point metabolite for aromatic amino acids and phenolic compounds.

This is an ancient eukaryotic pathway which has been subject to diverse evolutionary processes.

Several enzymes from these pathways are allosterically regulated by their end products: Phe, Tyr or Trp.

The shikimate pathway and aromatic amino acids, and the specialised metabolites derived from them, simultaneously respond to rhythmic changes.
Plant Light Stress
Authors: Osakabe Keishi , Osakabe Yuriko
Published: April 2013

Plants produce their own energy and metabolites via photosynthesis. Although photosynthesis requires sunlight, the very nature of sunlight also has a negative effect on photosynthesis. Plants have therefore evolved various protective and response mechanisms to mitigate the negative effects of light stress.

Key Concepts:

Photosynthesis causes a potential risk of photodamage.

Excess light and ultraviolet irradiation from sunlight lead to increased production of ROS, which cause photo‐oxidative damage.

Plants have evolved protective and response mechanisms against photodamage.

ROS can be utilised as a signalling molecule for response against light stress as well as other abiotic and biotic stresses.
Plant Storage Products (Carbohydrates, Oils and Proteins)
Authors: Kermode Allison R
Published: April 2013

The majority of foods consumed by humans and their domesticated animals as food sources are ultimately obtained from plants, especially seeds. The storage products in seeds are predominately carbohydrates, oils and proteins, which are synthesised and stored in specialised tissues during seed development. Ultimately the storage products ensure successful establishment of the new plant, and the vigour of the young seedling. For example, the reserves are utilised following germination to support early growth of the seedling, allowing it to survive before it commences photosynthesis and autotrophic growth. Some of the storage compounds of seeds play a direct protective role, allowing the seed to withstand water loss during the final stages of its development, and to survive in the dry state for long periods under adverse environmental conditions. Molecular, proteomic and other approaches are elucidating the regulatory networks of genes and encoded proteins that underlie the biochemical and physiological basis of seed maturation, and the accumulation of stored compounds.

Key Concepts:

Seed proteins directly provide more than half of the global intake of dietary protein in humans.

In seeds, storage products (carbohydrates, oils and proteins) are accumulated during maturation and are utilised following germination to support early growth of the seedling. Likewise, storage products accumulated over winter in tree bark, tubers and perennial weed roots provide nutrients for rapid resumption of growth in the spring.

There are regulatory networks of genes and encoded proteins that control the accumulation of stored compounds during seed maturation.

Some of the storage products accumulated in seeds and plants are related to their longevity and protect them against environmental stresses.

The genetic engineering of the storage products of seeds and plants is directed towards improving their nutritional, stability and food processing properties.
Histamine Biosynthesis and Function
Authors: Ichikawa Atsushi , Tanaka Satoshi
Published: April 2013

Histamine is one of the essential biogenic amines that mediate a wide variety of physiological and pathological responses, such as inflammation, gastric acid secretion, neurotransmission and immune modulation. Histamine is synthesised through decarboxylation of
l
‐histidine and functions by acting on its specific receptors consisting of H
1
, H
2
, H
3
and H
4
subtypes. Mast cells and basophils store histamine in their cytoplasmic granules and release it when stimulated, whereas histamine release is closely associated with its

de novo

synthesis in gastric enterochromaffin‐like cells, and neurons. A series of antagonists targeting H
1
and H
2
subtype has brought about enormous success to therapies for immediate allergy and peptic ulcer, respectively. The H
3
subtype has been focused on as the therapeutic target for cognitive dysfunctions, because it is expressed preferentially in neurons and modulates the neurotransmitter release. Recently identified H
4
subtype is expressed preferentially in blood cells and mediates their chemotaxis in response to histamine.

Key Concepts:

Histamine mediates a wide variety of physiological and pathological responses, such as inflammation, gastric acid secretion, neurotransmission and immune modulation.

Histamine is synthesised through decarboxylation of
l
‐histidine by histidine decarboxylase and is catabolised through oxidative deamination or methylation.

Tissue histamine levels are transiently increased by degranulation of mast cells and basophils while they are upregulated by
de novo
synthesis in gastric enterochromaffin‐like cells, and neurons.

Histamine exerts its functions by acting on its specific receptors consisting of H
1
, H
2
, H
3
and H
4
receptors.

Histamine is a paracrine mediator, of which actions are generally limited in the local microenvironment.

Histamine H
1
receptor antagonists have brought successful therapeutic approaches for immediate allergy, because histamine evokes vasodilation and increased vascular permeability by acting on the H
1
receptor.

In the central nervous system, histamine is involved in awakening, appetite, maintenance of circadian rhythm, learning and memory, which are regulated by the H
1
and H
3
receptors.

Histamine stimulates parietal cells to induce gastric acid secretion by acting on the H
2
receptor, of which antagonists drastically improved therapeutic approaches for peptic ulcer.

Pre‐synaptic histamine H
3
receptor regulates release of various neurotransmitters including histamine itself, and is expected as a potential drug target for the treatment of cognitive dysfunctions.

Histamine H
4
receptor is expressed exclusively in blood cells and mediates their chemotaxis in response to histamine.
Tumours: Targeting of Monoclonal Antibodies for Imaging and Potential for Therapy
Authors: Kaur Sukhwinder , Jain Maneesh , Senapati Shantibhushan , Batra Surinder K
Published: April 2013

Antibodies by virtue of their unmatched specificity and diverse modes of action are the central components of the immune system to detect and combat pathogenic and nonpathogenic diseases. From the era of polyclonal antibodies to fully humanised monoclonal antibodies, a lot has been understood regarding their causal generation, molecular buildup, varied functioning and clearance from the biological system. This information has led to their widespread use in various arenas of pathogenesis including parasitic, bacterial and viral infections, heart diseases, autoimmune diseases and cancer. Since cancer derives from self, it is both difficult to diagnose as well as treat. With over 20 antibody‐based drugs now in use and over 100 in clinical trials for cancer, antibodies form the basis of several diagnostic as well as therapeutic modalities for some lethal malignancies. Further, antibody engineering to improve their characteristics, such as pharmacokinetics, has made them a major attraction for the biopharmaceutical industry.

Key Concepts:

The efficacy of murine monoclonal antibodies is limited by the inefficient action of the murine‐derived constant region and human anti‐mouse antibody response, resulting in their rapid clearance from the blood.

The success of an antibody‐based biopharmaceutical depends upon target antigen (location, distribution and density), targeted site (solid or haematological malignancy, tumour microenvironment) and targeting antibody (specificity, affinity, avidity, mode of action, origin and isotype).

Antitumour antibodies mediate their effector functions by antibody‐dependent cellular cytotoxicity, complement‐dependent cytotoxicity and antibody‐dependent cellular phagocytosis.

Antigenic heterogeneity, lack of tumour specificity, immunogenicity and nonuniform distribution of antibodies to the targeted site are major hurdles in successful use of antibody‐based therapeutics for solid tumours.

Antibodies against molecules inhibiting effector functions of helper and cytotoxic T cells improve the efficacy of an antitumour immune response.

Antibodies directed against co‐stimulatory receptors act as surrogate ligands and boost weak, ineffectual and endogenous antitumour immune responses.
Lesch–Nyhan Syndrome
Authors: Nyhan William L
Published: April 2013

Lesch–Nyhan syndrome is a dramatic X‐linked disease caused by deficient activity of the purine‐salvage enzyme
hypoxanthine–guanine
phosphoribosyltransferase (HPRT), leading to hyperuricemia and all of its clinical consequences. These manifestations, which the disease shares with gout, include hematuria, renal calculi, renal failure resulting from urate deposition in the parenchyma of the kidney, acute very painful arthritis, and tophaceous deposits in the cartilage of joints and the ears. The disease also includes a neurologic syndrome in which dystonia and its involuntary movements are associated with spasticity, making most patients wheelchair bound. Behavioural manifestations, possibly the most memorable feature of the disease, include self‐injurious behaviour. This takes a spectrum of forms, the most drastic of which is biting which leads to loss of tissue. The activity of the enzyme is readily measured in red blood cells. In the classic syndrome the activity is zero.

Key Concepts:

Lesch–Nyhan disease was the first example of a stereotyped pattern of abnormal behaviour in which there was a fundamental molecular etiology, the absence of activity of an enzyme.

The disease led to the development of the concept of behavioural phenotypes, and the coining of this phrase.

The gene is located on the X chromosome, and its expression in disease is almost exclusively in males.

Mutations in the gene represent the entire spectrum from missense and nonsense mutations to large deletions, and the rule in any family is for the mutation to be private.

The discovery of allopurinol, which lowers uric acid concentrations by inhibiting xanthine oxidase, has changed the pattern of disease from one of death in early infancy to childhood; now there are adults with the disease.

Successful treatment for neurologic and behavioural features of the disease has been elusive.

The enzyme is active in every cell. This fact has permitted some control of the disease in a family by heterozygote detection and pre‐natal diagnosis.

Heterozygote detection and pre‐natal diagnosis may be made by mutational analysis if mutation in the proband is known.
Dinosauria (Dinosaurs)
Authors: Carpenter Kenneth
Published: April 2013

Dinosaurs are a group of extinct vertebrates that lived from 230 to 65 million years ago (Ma). They originated in southern Pangaea during the Middle Triassic from a small, meter‐long bipedal archosaur (the group that includes crocodiles and pterosaurs). Within a few million years dinosaurs rapidly diversified into two major groups (Ornithischia and Saurischia) based on pelvic structure and three main clades or subgroups (Ornithischia, Sauropodomorpha and Theropoda). Further diversification resulted in the various dinosaur classic types, such as tyrannosaurs, apatosaurs, stegosaurs, ankylosaurs and ceratopsians. These various types reflect the two locomotor styles, bipedal and quadrupedal, as well as the three dietary groups, herbivorous, carnivorous and omnivorous. Dinosaurs spread globally and by the Jurassic appear on all the continents, including ice‐free Antarctica. They also spread into a variety of niches, including flight. The extinction of this seemingly successful group 65 Ma is still the subject of much debate. Hypothetical causes include disease, volcanism, sea level drop, asteroid impact, or a combination of these. The only survivor of the ‘Great Extinction’ are the birds, or avian dinosaurs.

Key Concepts:

Dinosaurs appeared in the Late Triassic of South America 230 Ma and survive today as birds.

Dinosaurs underwent dramatic diversification within a few million years after their appearance so that most varieties were present by the Middle Jurassic.

Dinosaurs also spread globally, occurring on all continents and in a variety of environments.

Although an asteroid impact apparently marks the end of the Cretaceous, there is still no uniform agreement that it was the cause for the extinction of nonavian dinosaurs.

Modern birds are believed to be descendants of small, feathered theropods.
Palaeognathae
Authors: Dyke Gareth J , Leonard Leona M
Published: April 2013

Current evolutionary consensus, based on both molecular and morphological data, suggests that there are two broad subdivisions at the base of living birds (Neornithes), the neognaths (Neognathae) and palaeognathous birds (Palaeognathae). Palaeognaths are characterised by their primitive skull morphology and a secondarily acquired characteristic – flightlessness. The group, as traditionally defined and still recognised by phylogenetic analyses, includes flightless birds (ostrich, rhea, emu, cassowaries and kiwis) and flighted tinamous. Flightless forms are found today on the former landmasses of Gondwana, Africa, South America and Australia, whereas tinamous are restricted to South America. Traditionally, palaeognaths have been subdivided into ratites (all the large flightless groundbirds) and tinamous, although some data sets suggest that this classification might be overly simplistic: Recent molecular studies have concluded that the South American flighted taxa are nested within the traditional ratite grouping. This is interesting because it means that ratite flightlessness has evolved convergently at least four times.

Key Concepts:

The evolutionary relationships of living birds (clade Neornithes) remain poorly resolved despite more than a century and a half of investigation.

Palaeognaths (Palaeognathae) comprise the large, flightless living ratites (emu, ostrich, cassowary and rhea) and their smaller, flying cousins; tinamou.

The fossil record of palaeognaths shows that this group was once made up of medium‐sized flying birds, the oldest currently known from the Paleocene (ca.60 million years ago (Ma)).

Palaeognaths are widely considered by biologists and palaeontologists to be the sister‐group of Neognaths, the clade that includes all other living birds.
Eutheria (Placental Mammals)
Authors: Archibald J David
Published: April 2013

Eutheria includes one of three major clades of mammals, the extant members of which are referred to as placentals.

With almost 4800 extinct and extant genera, including 1135 extant (living) genera and over 5000 extant species arrayed in 20 extant orders, placentals (extant eutherians) are the most taxonomically diverse of the three branches of extant mammals. Eutherians appear in the fossil record by 105 Ma (million years ago) and possibly by 160 Ma. Extant orders of eutherians (placentals) do not occur in the fossil record until after dinosaur extinction 65–66 Ma. Molecular studies generally agree with these dates for the origin of placental orders, but place the origin of Eutheria at approximately 190 Ma and groups related to living orders of mammals by 100 Ma. Placentals vary greatly in size (whales down to shrews), in locomotion (flying, swimming, climbing, burrowing, running, etc.), and diet (meat, leaves, fruit, termites, etc.). They have a high resting temperature (homiothermy) and produce this heat internally (endothermy). They have a chorioallantoic placenta that allows a long gestation for development.

Key Concepts:

Eutherian mammals arose somewhere between 105 and 190 Ma.

Extant eutherian mammals, known as placentals, may have originated as long as 100 Ma based on molecular studies.

Placental orders first began to appear and diversify approximately 65 Ma (±10 My) based on both molecular and fossil studies.

There are 20 orders of placentals comprised of 1135 living genera and over 5000 species.

Placentals have a high resting temperature (homiothermy) and produce this heat internally (endothermy).

Placentals have a chorioallantoic placenta that allows a long gestation for development, hence their name.

Placentals are arguably the most ecologically diverse group of living vertebrates as they vary greatly in size, locomotory types, and diet.
New World Monkeys
Authors: Rosenberger Alfred L , Hartwig Walter Carl
Published: April 2013

New World monkeys are the nonhuman primates of South and Central America. Because almost all of their evolutionary history took place on the island continent of South America without competition from other primates, and most likely in a strictly arboreal setting, the character of their adaptation is unique. Fossils and molecules indicate the major lineages are long enduring, having attained diverse, stable ecological conditions quite early. Today, platyrrhine (wide‐nosed) monkeys comprise the most diversified taxonomic group among anthropoids. More primitive anatomically than Old World monkeys or apes, some forms resemble early fossil anthropoids from Egypt and serve well as models for reconstructing their behaviour. Others are more like the specialised apes in their locomotor adaptations, or the modified, folivorous leaf monkeys, whereas some evoke the big‐brained, extractive foraging strategies of African apes. Highly varied in their outward appearance as well, the range of social behaviours and mating strategies exhibited by platyrrhines is without equal among the primates.

Key Concepts:

New World monkeys occupy a wide variety of arboreal niches in the seasonally flooded forests of the Amazon and Orinoco river systems in continental South America, as well as more peripheral and less tropical biomes in southern South America, Central America and the Caribbean.

Living New World monkeys are the smallest anthropoid primates, ranging across a span from less than 1 kg to approximately 10 kg.

As an isolated, highly diversified radiation they are important models for studying parallel evolution in anatomy and behaviour while also providing living analogies for reconstructing the adaptations of extinct primates.

The adaptive radiation of platyrrhines unfolded along cladistic lines, with each of the four main lineages occupying a distinct ecological zone characterised by a combination of body size, feeding preference and locomotor habit.

The four main branches of the platyrrhine radiation, and some of the living genera, are older than any of the lineages or genera of Old World monkeys or apes.

Where platyrrhines originally came from, directly from Africa or via North America, remains a difficult question as both hypotheses have their own pros and cons.

The modern radiation of New World monkeys is an Amazonian phenomenon that was taking root 11–13 million years ago, as shown by fossils from a rich site in Colombia, but older, more primitive forms are found in Patagonia.

Because of their dependence on multi‐level tropical forest ecosystems, New World monkey species are under acute threat of extinction as humans occupy and consume more and more forested areas and resources.
Sirenia (Dugongs and Manatees)
Authors: Domning Daryl P
Published: April 2013

Sirenia are an order of large, aquatic, plant‐eating, mostly tropical placental mammals that includes the modern seacows (dugongs and manatees) and their extinct relatives. Their nearest living relatives are the Proboscidea (elephants). Together with some extinct orders (including Desmostylia and Embrithopoda), Sirenia and Proboscidea make up a group known as Tethytheria, after their likely origin along the shores of the ancient Tethys Seaway in the Old World. Sirenians first appeared in the fossil record in the Eocene. They comprise four families, two extinct (Prorastomidae and Protosirenidae, both Eocene) and two extant (Trichechidae and Dugongidae). For most of the Tertiary, they formed multispecies communities in marine environments, partitioning seagrass resources in ways not completely understood. However, global cooling after the middle Miocene, and human predation in the North Pacific, diminished their diversity to only two living genera and four species.

Key Concepts:

Sirenians are herbivorous, completely aquatic mammals that evolved from land‐dwelling ancestors.

The closest living relatives of the Sirenia are the Proboscidea (elephants).

Sirenians have a fossil record dating from the Eocene.

Most sirenians of the past lived in salt water, and fed on seagrasses (marine flowering plants).

The Family Dugongidae was the most diverse and successful family of sirenians.

Several lineages of sirenians apparently specialised on eating large seagrass rhizomes, using bladelike, self‐sharpening upper tusks.

These specialised sirenians could act as ‘keystone species’, allowing both seagrasses and other kinds of sirenians to become locally more diverse.

Unlike today, sirenians of the past formed communities of several coexisting species, with a different taxonomic makeup in each ocean basin.

Diversity of sirenians diminished after the middle Miocene, due to global cooling.

Manatees in the southeastern U.S. and Caribbean had a complicated history during the Pleistocene Ice Ages, shifting their range south and north with the alternating glacial and interglacial cycles.
Nematoda (Roundworms)
Authors: Poinar George
Published: April 2013

The Nematoda are a group of nonsegmented worm‐like invertebrates that occur worldwide in a wide range of habitats, including fresh and salt waters, soil, plants and animals. They are one of the most abundant group of invertebrates on the face of the earth and rival the arthropods in biodiversity and species abundance. Their estimated numbers range from 1.5 billion in an upper 20 mm in 1.6 hectares of marine beach sand to 380 million in a square metre of leaf litter. Evidence from fossils and extant forms indicate that they evolved in the sea and came on land by probably moving up brackish estuaries into freshwater habitats. Although many of the plant parasites are considered pests and controlled with nematicides, other nematodes are important in controlling agricultural and medically important insect pests and still others have been used as experimental organisms in genetics.

Key Concepts:

Nematodes are the most successful group of the Ecdysoma, or pseudocoelomate bilateria.

Nematodes are one of the most abundant groups of invertebrates.

Some 20 000 nematode species have been described.

Estimates for species diversity range from 100 000 to 10 million.

Plant parasitic nematodes can be important agricultural pests.

Many nematodes live in the bodies of humans and their pets.
Myriapoda (Including Centipedes and Millipedes)
Authors: Wright Jonathan C
Published: April 2013

The Myriapoda comprises four classes of terrestrial arthropods: Chilopoda or centipedes, Diplopoda or millipedes, Symphyla and Pauropoda. Myriapods are generally found in soil and litter and have a worldwide distribution. Approximately 13 000 species are known. Myriapods share a five‐ or six‐segmented head, a single pair of antennae, uniramous (unbranched) limbs and an elongate trunk without obvious tagmatisation. The Chilopoda and Diplopoda are the largest classes, numbering respectively approximately 3000 and 10 000 described species. Centipedes are carnivorous and share poison claws derived from the first pair of trunk limbs, whereas the other classes are primarily detritivores and may be significant contributors to litter breakdown and nutrient turnover. Recent molecular phylogenetic studies indicate that the Myriapoda comprise a monophyletic group and a sister taxon to the Pancrustacea (Crustacea and Insecta). They were among the first animals to colonise land.

Key Concepts:

Myriapoda comprise four classes of terrestrial arthropods: Chilopoda (centipedes), Diplopoda (millipedes), Symphyla and Pauropoda.

Centipedes are carnivorous, possessing unique poison claws on the first trunk (post head) segment.

Millipedes are characterised by diplosegments – pairs of trunk segments sharing a single tergal plate.

Millipedes, symphylans and pauropods are detritivores, occurring primarily in soils and leaf litter.

Myriapods have separate sexes (gonochoristic), and sperm transfer generally involves the exchange of one or more spermatophores via specialised appendages.

Molecular phylogenetic evidence supports monophyly of the Myriapoda, with the Myriapoda probably comprising a sister taxon to the Pancrustacea (Crustacea and Insecta).

Both centipedes and millipedes have fossil records dating back to the mid‐upper Silurian (ca. 420 mya) and probably colonised land prior to insects.

Myriapods and insects share several derived traits representing adaptations to land: tracheal systems, predominantly uniramous (unbranched) limbs and excretory Malpighian tubules opening into the hindgut.
Bryozoa (Ectoprocta: ‘Moss’ Animals)
Authors: Claus Nielsen
Published: April 2013

The Bryozoa are a phylum of small, colonial, filter‐feeding, almost exclusively sessile, aquatic organisms. Approximately 5600 living species have been described, and the fossil record comprises approximately 20 000 species. Bryozoans are found in all oceans and many freshwater areas. Most species encrust stones or algae, others form erect bushes and a few form free‐living colonies. The individuals in the colonies are almost always smaller than 1 mm, but colonies of freshwater species may grow to 0.5 m in diameter, and some of the marine species form tufts up to more than 25 cm in length. Each individual (zooid) in a colony consists of rather stiff, often calcified, main body wall (cystid) and a tentacle crown plus gut (polypide), which can be retracted into the cystid. Colonies are hermaphroditic, in some groups with hermaphroditic zooids, but a number of groups have separate male and female zooids. Development is indirect with triangular shelled cyphonautes larvae in a few groups, but brood protection and lecithotrophic larvae of many types are more widespread.

Key Concepts:

Bryozoans are colonial aquatic organisms most often growing on stones, shells or algae.

Each individual (zooid) in a colony consists of a more or less stiff main body wall (cystid) and a retractable tentacle crown around the mouth and a gut (polypide), which can be retracted into the cystid.

The almost cylindrical tentacles have bands of cilia which create a water current towards the mouth and between the tentacles. Food particles are strained from this water current.

Colonies are hermaphroditic; many species show hermaphroditic zooids, but some show male and female zooids.

Most species brood the embryos in more or less elaborate brooding structures, called ovicels in the cheilostomes; cyclostomes have large female zooids, which are brood chambers with a rudimentary polypide.

The Bryozoa can be classified as follows: Bryozoa (Phylactolaemata+Gymnolaemata (Eurystomata (Cheilostomata+Ctenostomata)+Cyclostomata)).
Fossils and Fossilisation
Authors: Brett Carlton E , Thomka James R
Published: April 2013

Fossils are the recognisable remains or traces of activity of prehistoric life, typically defined as >10 000 years old. Pseudofossils are nonorganic objects that bear false resemblance to organism remains. The fossil record is strongly biased toward organisms with hard parts, such as mineralised skeletons of calcite, aragonite, phosphate, silica or refractory organic materials such as wood, that live in areas prone to pulses of sediment accumulation. Hence, preservation is not only particularly favoured in shallow offshore, storm‐affected and marine environments but also to a lesser extent, in the deep sea, lakes and river point bars. Occasionally, rapid burial in anoxic setting coupled with early mineralisation leads to extraordinarily preserved fossil Lagerstätten. The study of fossil preservation – taphonomy – is subdivided into biostratinomy and fossil diagenesis. Biostratinomic processes affect potential fossil remains between death and final burial, including decay of organic parts, disarticulation, fragmentation, abrasion, bioerosion and dissolution. Fossil diagenesis constitutes processes that affect organic remains subsequent to burial such as dissolution, compaction and early and late mineralisation. Taphonomy reveals biases of the fossil record and also provides insights into depositional rates and processes.

Key Concepts:

Fossils are prehistoric (>10 000 years), discrete remains or traces of behaviour of once‐living organisms.

Preservation in the fossil record is a rare event that generally requires organisms with ‘hard parts’ (mineralised or resistant organic skeletons) and entombment within sediments.

Extraordinary preservation of articulated skeletons and even soft parts requires very rapid burial, often associated with mass mortalities, in low oxygen sediments and various types of early diagenetic mineralisation.

A variety of settings may favour exceptional preservation, including storm‐influenced continental shelves, deeper marine environments and stagnant lagoons, freshwater lakes, including maars or volcanic lakes, caves, tar pits and permafrost.

The study of fossil preservation, taphonomy, is subdivided into biostratinomy and fossil diagenesis.

Biostratinomy comprises the study of all processes that affect potential fossils from the time of death, or production of a trace or sheddable structures (leaves, seed and exoskeletal parts), to final burial.

Biostratinomic processes include decay of soft parts, infilling by disarticulation of bivalved or multielement skeletons, breakage, bioerosion, abrasion, transport and chemical corrosion.

Fossil diagenesis includes compaction, early mineralisation of various sorts including infillings and/or replacements of pyrite, phosphate, and silica and late‐stage mineralisation including overgrowth of earlier‐formed minerals and major episodes of (sometimes selective) dissolution.

A combination of biostratinomic and diagenetic characteristics can aid in identifying taphonomically defined assemblages or taphofacies that may provide a ‘fingerprint’ of particular depositional environments.
Terrestrialisation (Precambrian–Devonian)
Authors: Selden Paul
Published: April 2013

The emergence of plants and animals from the sea on to land – terrestrialisation – was one of the major advances in the history of life on Earth. Evidence for early colonisation is poor, but the fossil record reveals that by mid‐Palaeozoic times, complex terrestrial ecosystems had become established. The first phase of land colonisation by organisms may have started in the Precambrian, some 2.6 gigaannums (Ga) ago, in the form of microbially bound alluvial sands. The second phase began in earnest in Ordovician times, when early land plants, in the form of bryophyte‐like spores, first appear in the fossil record. By the Silurian, true vascular plants were present, and these green swards were inhabited by mainly detritivorous and predatory arthropods. By the late Devonian, true forests had developed, but it was not until the latest Palaeozoic that modern‐type terrestrial ecosystems, with abundant herbivores in the food chain.

Key Concepts:

Organisms need to be overcome many physiological barriers when colonising the land from the sea.

Conditions on the early Earth (∼4.6–1.0 Ga) were inhospitable to terrestrial life.

Microbial crusts were likely the earliest land life.

Higher plants appeared on land in the Ordovician period; vascular plants in the Silurian.

The first land animals (Silurian) were detritivorous and predatory arthropods.

Modern‐type ecosystems, with abundant herbivory and vertebrates, came in the latest Palaeozoic.
Extinction: End‐Triassic Mass Extinction
Authors: Hautmann Michael
Published: April 2013

One of the five greatest mass extinction events in Earth's history occurred at the end of the Triassic,c.200 million years ago. This event ultimately eliminated conodonts and nearly annihilated corals, sphinctozoan sponges and ammonoids. Other strongly affected marine taxa include brachiopods, bivalves, gastropods and foraminifers. On the land, there is evidence for a temporal disturbance of plant communities but only few plant taxa finally disappeared. Terrestrial vertebrates also suffered but timing and extent of this extinction remains equivocal. The cause of the end‐Triassic mass extinction was probably linked to the contemporary activity of the Central Atlantic Magmatic Province, which heralded the breakup of the supercontinent Pangaea. Possible kill mechanisms associated with magmatic activity include sea‐level changes, marina anoxia, climatic changes, release of toxic compounds and acidification of seawater. Remarkably, long‐term effects on marine biota were rather different between ecological groups: a nearly instantaneous recovery of level‐bottom communities is contrasted by the virtual absence of reef systems for nearly 10 million years after the extinction event.

Key Concepts:

Nearly half of all marine genera and a smaller but still significant proportion of terrestrial taxa went extinct at the end of the Triassic period,c.200 million years ago.

The end‐Triassic mass extinction took place during a geologically short time interval, which coincided with the onset of massive magmatic extrusions along fracture zones of the disassembling supercontinent Pangaea.

A cause‐and‐effect relationship between magmatic activity and mass extinction is indicated by the accordance of predicted extinction patterns and observed data from the fossil record.

Ocean acidification as a kill mechanism in marine ecosystems is confirmed by preferential extinction of taxa with thick aragonitic skeletons.

The end‐Triassic mass extinction event provides a test‐case for studying evolutionary responses to major environmental disturbances on the global scale and over geological time.

Although there are differences in emission rates, the massive magmatic CO2release at the end of the Triassic is quantitatively similar to a potential release by complete combustion of the global fossil fuel reserves.

A provisional prediction from the data of the fossil record is that in the marine realm level‐bottom communities are able to recover much more quickly from the effects of excess CO2than reef systems.
Geographical Variation
Authors: Olvido Alexander E , Mousseau Timothy A
Published: April 2013

Geographical variation refers to differences among populations in genetically based traits across the natural geographic range of a species. Understanding the factors that give rise to and maintain geographical variation helps elucidate the causes and consequences of evolution. In the simplest case, we divide these factors into purely genetic versus environmental components to tease apart their relative contributions to observed phenotypic variation. Subsequent experiments allow us to partition further the genetic components of phenotypic variation towards a molecular understanding, hopefully to reveal the actualdeoxyribonucleic acid(DNA)‐scale changes giving rise to adaptations we see at the population level. Studies of a select number of organisms – all of which begin with geographic variation – demonstrate this highly productive strategy. Given its relevance to differentiation among populations, geographic variation also has direct bearing on the question of species origins.

Key Concepts:

Geographical variation refers to differences among populations of organisms in genetically based traits across the natural geographic range of that species.

Understanding how initial population size, gene flow, mutation frequency, and environmental (abiotic) factors give rise to and maintain geographical variation can shed light on direction and rate of evolutionary change.

Clinal variation – a form of geographic variation – suggests past or present action of natural selection.

Reciprocal transplantation and ‘common garden’ experiments are two effective manipulations that can reveal genetically based phenotypic variation.

A number of studies of geographic variation, including those about sickle‐cell anaemia, warfarin‐resistance, and lepidopteran colouration, have shifted to a more molecular focus.

A number of other studies attempt to understand geographic variation in the broader context of community and ecosystem structure.

Given the multi‐faceted approach to understanding it, geographic variation can help address the question of species’ origins.
Species and Speciation: Overview
Authors: Shaw Kerry L
Published: April 2013

The species is the fundamental or basic unit of organic or biological diversity, usually characterised as a group of individuals or populations of individuals with interbreeding or genealogical relationships. Understanding the nature of species can be challenging when considering sexual versus asexual organisms. Identifying species is also challenging, for example, when studying the fossil record, or when speciation is not yet complete. Speciation is the process leading to the formation or origin of species. As such, speciation is the process by which reproductive and/or genealogical boundaries form around groups of organisms. Commonly understood forces of evolution causing divergence in phenotypes contribute to the formation of species. Geographic, ecological, behavioural and genetic factors are also important to understanding how the process works.

Key Concepts:

Species are fundamental units of biodiversity but can be defined in different ways, from either a prospective (future) or retrospective (historical) perspective.

Speciation is the study of how new species form and may be brought about by a multitude of phenotypic changes.

The causes of speciation are complex and likely include a diversity of evolutionary forces such as natural selection, sexual selection and genetic drift that lead to divergence in phenotype.

Divergence in specific phenotypes is important to speciation if they directly or indirectly cause a reduction in gene flow between newly forming species.

The genetics of speciation is the study of the genetic basis of phenotypic evolution that leads to a reduction in gene flow between newly forming species.