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Mammal Digestion
Mammals (class Mammalia from Latin mamma "breast") are a clade of endothermic amniotes distinguished from reptiles and birds by the possession of a neocortex (a region of the brain), hair, three middle ear bones and mammary glands.

Mammals include the largest animals on the planet, the great whales, as well as some of the most intelligent, such as elephants, primates and cetaceans. The basic body type is a terrestrial quadruped, but some mammals are adapted for life at sea, in the air, in trees, underground or on two legs. The largest group of mammals, the placentals, have a placenta, which enables the feeding of the fetus during gestation.

Mammals range in size from the 30 – bumblebee bat to the 33 m blue whale. With the exception of the five species of monotreme (egg-laying mammals), all modern mammals give birth to live young. Most mammals, including the six most species-rich orders, belong to the placental group. The three largest orders in number of species are Rodentia: mice, rats, porcupines, beavers, capybaras and other gnawing mammals; Chiroptera: bats; and Soricomorpha: shrews, moles and solenodons. The next three biggest orders, depending on the biological classification scheme used, are the Primates including the great apes and monkeys; the Cetartiodactyla including whales and even-toed ungulates; and the Carnivora which includes cats, dogs, weasels, bears and seals.

The word "mammal" is modern, from the scientific name Mammalia, coined by Carl Linnaeus in 1758, derived from the Latin mamma ("teat, pap"). All female mammals nurse their young with milk, which is secreted from special glands, the mammary glands. According to Mammal Species of the World, 5,416 species were known in 2006. These were grouped in 1,229 genera, 153 families and 29 orders. In 2008 the International Union for Conservation of Nature (IUCN) completed a five-year, 1,700-scientist Global Mammal Assessment for its IUCN Red List, which counted 5,488 species. In some classifications, extant mammals are divided into two subclasses: the Prototheria, that is, the order Monotremata; and the Theria, or the infraclasses Metatheria and Eutheria. The marsupials constitute the crown group of the Metatheria, and include all living metatherians as well as many extinct ones; the placentals are the crown group of the Eutheria. While mammal classification at the family level has been relatively stable, several contending classifications regarding the higher levels—subclass, infraclass and order, especially of the marsupials—appear in contemporaneous literature. Much of the changes reflect the advances of cladistic analysis and molecular genetics. Findings from molecular genetics, for example, have prompted adopting new groups, such as the Afrotheria, and abandoning traditional groups, such as the Insectivora.

The early synapsid mammalian ancestors were sphenacodont pelycosaurs, a group that produced the non-mammalian Dimetrodon. At the end of the Carboniferous period, this group diverged from the sauropsid line that led to today's reptiles and birds. The line following the stem group Sphenacodontia split-off several diverse groups of non-mammalian synapsids—sometimes referred to as mammal-like reptiles—before giving rise to the proto-mammals (Therapsida) in the early Mesozoic era. The modern mammalian orders arose in the Paleogene and Neogene periods of the Cenozoic era, after the extinction of non-avian dinosaurs, and have been among the dominant terrestrial animal groups from 66 million years ago to the present.

Classification

Mammal classification has been through several iterations since Carl Linnaeus initially defined the class. No classification system is universally accepted; McKenna & Bell (1997) and  Wilson & Reader (2005) provide useful recent compendiums.  George Gaylord Simpson's "Principles of Classification and a Classification of Mammals" (AMNH Bulletin v. 85, 1945) provides systematics of mammal origins and relationships that were universally taught until the end of the 20th century. Since Simpson's classification, the paleontological record has been recalibrated, and the intervening years have seen much debate and progress concerning the theoretical underpinnings of systematization itself, partly through the new concept of cladistics. Though field work gradually made Simpson's classification outdated, it remained the closest thing to an official classification of mammals.

Definitions 

The word "mammal" is modern, from the scientific name Mammalia coined by Carl Linnaeus in 1758, derived from the Latin mamma ("teat, pap"). In an influential 1988 paper, Timothy Rowe defined Mammalia phylogenetically as the crown group of mammals, the clade consisting of the most recent common ancestor of living monotremes (echidnas and platypuses) and therian mammals (marsupials and placentals) and all descendants of that ancestor.  Since this ancestor lived in the Jurassic period, Rowe's definition excludes all animals from the earlier Triassic, despite the fact that Triassic fossils in the Haramiyida have been referred to the Mammalia since the mid-19th century.  If Mammalia is considered as the crown group, its origin can be roughly dated as the first known appearance of animals more closely related to some extant mammals than to others. Ambondro is more closely related to monotremes than to therian mammals while Amphilestes and Amphitherium are more closely related to the therians; as fossils of all three genera are dated about  in the Middle Jurassic, this is a reasonable estimate for the appearance of the crown group. 

T. S. Kemp has provided a more traditional definition: "synapsids that possess a dentary–squamosal jaw articulation and occlusion between upper and lower molars with a transverse component to the movement" or, equivalently in Kemp's view, the clade originating with the last common ancestor of Sinoconodon and living mammals.  The earliest known synapsid satisfying Kemp's definitions is Tikitherium, dated , so the appearance of mammals in this broader sense can be given this Late Triassic date.  

McKenna/Bell classification

In 1997, the mammals were comprehensively revised by Malcolm C. McKenna and Susan K. Bell, which has resulted in the McKenna/Bell classification. Their 1997 book, Classification of Mammals above the Species Level,  is a comprehensive work on the systematics, relationships and occurrences of all mammal taxa, living and extinct, down through the rank of genus, though molecular genetic data challenge several of the higher level groupings. The authors worked together as paleontologists at the American Museum of Natural History, New York. McKenna inherited the project from Simpson and, with Bell, constructed a completely updated hierarchical system, covering living and extinct taxa that reflects the historical genealogy of Mammalia.

Extinct groups are represented by a dagger (†).

Class Mammalia
*Subclass Prototheria: monotremes: echidnas and the platypus
*Subclass Theriiformes: live-bearing mammals and their prehistoric relatives
**Infraclass †Allotheria: multituberculates
**Infraclass †Eutriconodonta: eutriconodonts
**Infraclass Holotheria: modern live-bearing mammals and their prehistoric relatives
***Superlegion †Kuehneotheria
***Supercohort Theria: live-bearing mammals
****Cohort Marsupialia: marsupials
*****Magnorder Australidelphia: Australian marsupials and the monito del monte
*****Magnorder Ameridelphia: New World marsupials. Now considered paraphyletic, with shrew opossums being closer to australidelphians.  
****Cohort Placentalia: placentals
*****Magnorder Xenarthra: xenarthrans
*****Magnorder Epitheria: epitheres
******Superorder Anagalida: lagomorphs, rodents and elephant shrews
******Superorder Ferae: carnivorans, pangolins, †creodonts and relatives
******Superorder Lipotyphla: insectivorans
******Superorder Archonta: bats, primates, colugos and treeshrews
******Superorder Ungulata: ungulates
*******Order Tubulidentata incertae sedis: aardvark
*******Mirorder Eparctocyona: †condylarths, whales and artiodactyls (even-toed ungulates)
*******Mirorder †Meridiungulata: South American ungulates
*******Mirorder Altungulata: perissodactyls (odd-toed ungulates), elephants, manatees and hyraxes

Molecular classification of placentals

Molecular studies based on DNA analysis have suggested new relationships among mammal families over the last few years. Most of these findings have been independently validated by retrotransposon presence/absence data. Classification systems based on molecular studies reveal three major groups or lineages of placental mammals- Afrotheria, Xenarthra and Boreoeutheria- which diverged in the Cretaceous. The relationships between these three lineages is contentious, and all three possible different hypotheses have been proposed with respect to which group is basal. These hypotheses are Atlantogenata (basal Boreoeutheria), Epitheria (basal Xenarthra) and Exafroplacentalia (basal Afrotheria). Boreoeutheria in turn contains two major lineages- Euarchontoglires and Laurasiatheria.

Estimates for the divergence times between these three placental groups range from 105 to 120 million years ago, depending on type of DNA (such as nuclear or mitochondrial)  and varying interpretations of paleogeographic data.

Cladogram based on Tarver et al. (2016) 

Group I: Afrotheria
*Clade Afroinsectiphilia
**Order Macroscelidea: elephant shrews (Africa)
**Order Afrosoricida: tenrecs and golden moles (Africa)
**Order Tubulidentata: aardvark (Africa south of the Sahara)
*Clade Paenungulata
**Order Hyracoidea: hyraxes or dassies (Africa, Arabia)
**Order Proboscidea: elephants (Africa, Southeast Asia)
**Order Sirenia: dugong and manatees (cosmopolitan tropical)
Group II: Xenarthra
*Order Pilosa: sloths and anteaters (neotropical)
*Order Cingulata: armadillos and extinct relatives (Americas)
Group III: Boreoeutheria
*Clade: Euarchontoglires (Supraprimates)
**Superorder Euarchonta
***Order Scandentia: treeshrews (Southeast Asia).
***Order Dermoptera: flying lemurs or colugos (Southeast Asia)
***Order Primates: lemurs, bushbabies, monkeys, apes, humans (cosmopolitan)
**Superorder Glires
***Order Lagomorpha: pikas, rabbits, hares (Eurasia, Africa, Americas)
***Order Rodentia: rodents (cosmopolitan)
*Clade Laurasiatheria
**Order Eulipotyphla: shrews, hedgehogs, moles, solenodons
**Clade Ferungulata
***Clade Cetartiodactyla
****Order Cetacea: whales, dolphins and porpoises
****Order Artiodactyla: even-toed ungulates, including pigs, hippopotamus, camels, giraffe, deer, antelope, cattle, sheep, goats (Note that Artiodactyla is paraphyletic to Cetacea)
***Clade Pegasoferae
****Order Chiroptera: bats (cosmopolitan)
****Clade Zooamata
*****Order Perissodactyla: odd-toed ungulates, including horses, donkeys, zebras, tapirs and rhinoceroses
*****Clade Ferae
******Order Pholidota: pangolins or scaly anteaters (Africa, South Asia)
******Order Carnivora: carnivores (cosmopolitan), including cats and dogs

Statistics

Most mammals, including the six most species-rich orders, belong to the placental group. The three largest orders in numbers of species are Rodentia: mice, rats, porcupines, beavers, capybaras and other gnawing mammals; Chiroptera: bats; and Soricomorpha: shrews, moles and solenodons. The next three biggest orders, depending on the biological classification scheme used, are the Primates including the great apes and monkeys; the Cetartiodactyla including whales and even-toed ungulates; and the Carnivora which includes cats, dogs, weasels, bears and seals. According to Mammal Species of the World, 5,416 species were known in 2006. These were grouped in 1,229 genera, 153 families and 29 orders. In 2008 the International Union for Conservation of Nature (IUCN) completed a five-year, 1,700-scientist Global Mammal Assessment for its IUCN Red List, which counted 5,488 species. 

Evolutionary history

Synapsida, a clade that contains mammals and their extinct relatives, originated during the Pennsylvanian subperiod, when they split from reptilian and avian lineages. Crown group mammals evolved from earlier mammaliaforms during the Early Jurassic.

The cladogram following takes Mammalia to be the crown group.

Evolution from amniotes

The first fully terrestrial vertebrates were amniotes. Like their amphibious tetrapod predecessors, they had lungs and limbs. Amniotic eggs, however, have internal membranes that allow the developing embryo to breathe but keep water in. Hence, amniotes can lay eggs on dry land, while amphibians generally need to lay their eggs in water.

The first amniotes apparently arose in the Late Carboniferous. They descended from earlier reptiliomorph amphibious tetrapods,  which lived on land that was already inhabited by insects and other invertebrates as well as ferns, mosses and other plants. Within a few million years, two important amniote lineages became distinct: the synapsids, which would later include the common ancestor of the mammals; and the sauropsids, which now include turtles, lizards, snakes, crocodilians, dinosaurs and birds.  Synapsids have a single hole (temporal fenestra) low on each side of the skull. One synapsid group, the pelycosaurs, included the largest and fiercest animals of the early Permian.  Nonmammalian synapsids are sometimes called "mammal-like reptiles".

Therapsids descended from pelycosaurs in the Middle Permian, about 265 million years ago, and became the dominant land vertebrates. They differ from basal eupelycosaurs in several features of the skull and jaws, including: larger skulls and incisors which are equal in size in therapsids, but not for eupelycosaurs. The therapsid lineage leading to mammals went through a series of stages, beginning with animals that were very similar to their pelycosaur ancestors and ending with probainognathian cynodonts, some of which could easily be mistaken for mammals. Those stages were characterized by: 
*The gradual development of a bony secondary palate.
*Progression towards an erect limb posture, which would increase the animals' stamina by avoiding Carrier's constraint. But this process was slow and erratic: for example, all herbivorous nonmammaliaform therapsids retained sprawling limbs (some late forms may have had semierect hind limbs); Permian carnivorous therapsids had sprawling forelimbs, and some late Permian ones also had semisprawling hindlimbs. In fact, modern monotremes still have semisprawling limbs.
*The dentary gradually became the main bone of the lower jaw which, by the Triassic, progressed towards the fully mammalian jaw (the lower consisting only of the dentary) and middle ear (which is constructed by the bones that were previously used to construct the jaws of reptiles).

First mammals

The Permian–Triassic extinction event, which was a prolonged event due to the accumulation of several extinction pulses, ended the dominance of carnivores therapsids.  In the early Triassic, most medium to large land carnivore niches were taken over by archosaurs  which, over an extended period of time (35 million years), came to include the crocodylomorphs,  the pterosaurs and the dinosaurs;  however, large cynodonts like Trucidocynodon and traversodontids still occupied large sized carnivorous and herbivorous niches respectively. By the Jurassic, the dinosaurs had come to dominate the large terrestrial herbivore niches as well. 

The first mammals (in Kemp's sense) appeared in the Late Triassic epoch (about 225 million years ago), 40 million years after the first therapsids. They expanded out of their nocturnal insectivore niche from the mid-Jurassic onwards;  The Jurassic Castorocauda, for example, had adaptations for swimming, digging and catching fish.  Most, if not all, are thought to have remained nocturnal (the Nocturnal bottleneck), accounting for much of the typical mammalian traits.  The majority of the mammal species that existed in the Mesozoic Era were multituberculates, eutriconodonts and spalacotheriids. The earliest known metatherian is Sinodelphys, found in 125 million-year-old Early Cretaceous shale in China's northeastern Liaoning Province. The fossil is nearly complete and includes tufts of fur and imprints of soft tissues. 

The oldest known fossil among the Eutheria ("true beasts") is the small shrewlike  Juramaia sinensis, or "Jurassic mother from China", dated to 160 million years ago in the late Jurassic. A later eutherian, Eomaia, dated to 125 million years ago in the early Cretaceous, possessed some features in common with the marsupials but not with the placentals, evidence that these features were present in the last common ancestor of the two groups but were later lost in the placental lineage.  In particular, the epipubic bones extend forwards from the pelvis. These are not found in any modern placental, but they are found in marsupials, monotremes, nontherian mammals and Ukhaatherium, an early Cretaceous animal in the eutherian order Asioryctitheria. This also applies to the multituberculates.  They are apparently an ancestral feature, which subsequently disappeared in the placental lineage. These epipubic bones seem to function by stiffening the muscles during locomotion, reducing the amount of space being presented, which placentals require to contain their fetus during gestation periods. A narrow pelvic outlet indicates that the young were very small at birth and therefore pregnancy was short, as in modern marsupials. This suggests that the placenta was a later development.

The earliest known monotreme was Teinolophos, which lived about 120 million years ago in Australia.  Monotremes have some features which may be inherited from the original amniotes such as the same orifice to urinate, defecate and reproduce (cloaca) – as lizards and birds also do –  and they lay eggs which are leathery and uncalcified. 

Earliest appearances of features

Hadrocodium, whose fossils date from approximately 195 million years ago, in the early Jurassic, provides the first clear evidence of a jaw joint formed solely by the squamosal and dentary bones; there is no space in the jaw for the articular, a bone involved in the jaws of all early synapsids.

The earliest clear evidence of hair or fur is in fossils of Castorocauda, from 164 million years ago in the mid-Jurassic. In the 1950s, it was suggested that the foramina (passages) in the maxillae and premaxillae (bones in the front of the upper jaw) of cynodonts were channels which supplied blood vessels and nerves to vibrissae (whiskers) and so were evidence of hair or fur;   it was soon pointed out, however, that foramina do not necessarily show that an animal had vibrissae, as the modern lizard Tupinambis has foramina that are almost identical to those found in the nonmammalian cynodont Thrinaxodon.Bennett, A. F. and Ruben, J. A. (1986) "The metabolic and thermoregulatory status of therapsids"; pp. 207–218 in N. Hotton III, P. D. MacLean, J. J. Roth and E. C. Roth (eds), "The ecology and biology of mammal-like reptiles", Smithsonian Institution Press, Washington.  Popular sources, nevertheless, continue to attribute whiskers to Thrinaxodon.  Studies on Permian coprolites suggest that non-mammalian synapsids of the epoch already had fur, setting the evolution of hairs possibly as far back as dicynodonts.

When endothermy first appeared in the evolution of mammals is uncertain, though it is generally agreed to have first evolved in non-mammalian therapsids.  Modern monotremes have lower body temperatures and more variable metabolic rates than marsupials and placentals,  but there is evidence that some of their ancestors, perhaps including ancestors of the therians, may have had body temperatures like those of modern therians.  Likewise, some modern therians like afrotheres and xenarthrans have secondarily developed lower body temperatures. 

The evolution of erect limbs in mammals is incomplete — living and fossil monotremes have sprawling limbs. The parasagittal (nonsprawling) limb posture appeared sometime in the late Jurassic or early Cretaceous; it is found in the eutherian Eomaia and the metatherian Sinodelphys, both dated to 125 million years ago.  Epipubic bones, a feature that strongly influenced the reproduction of most mammal clades, are first found in Tritylodontidae, suggesting that it is a synapomorphy between them and mammaliformes. They are omnipresent in non-placental mammaliformes, though Megazostrodon and Erythrotherium appear to have lacked them. 

It has been suggested that the original function of lactation (milk production) was to keep eggs moist. Much of the argument is based on monotremes, the egg-laying mammals.  

Rise of the mammals

Mammals took over the medium- to large-sized ecological niches in the Cenozoic, after the Cretaceous–Paleogene extinction event emptied ecological space once filled by non-avian dinosaurs and other groups of reptiles.  Then mammals diversified very quickly; both birds and mammals show an exponential rise in diversity. For example, the earliest known bat dates from about 50 million years ago, only 16 million years after the extinction of the dinosaurs. 

Molecular phylogenetic studies suggest that most placental orders diverged about 100 to 85 million years ago and that modern families appeared in the period from the late Eocene through the Miocene.  However, no placental fossils have been found from before the end of the Cretaceous. The earliest undisputed fossils of placentals comes from the early Paleocene, after the extinction of the dinosaurs.  In particular, scientists have identified an early Paleocene animal named Protungulatum donnae as one of the first placental mammals.  The earliest known ancestor of primates is Archicebus achilles  from around 55 million years ago. This tiny primate weighed 20–30 grams (0.7–1.1 ounce) and could fit within a human palm.

Anatomy and morphology

Distinguishing features

Living mammal species can be identified by the presence of sweat glands, including those that are specialized to produce milk to nourish their young.  In classifying fossils, however, other features must be used, since soft tissue glands and many other features are not visible in fossils. 

Many traits shared by all living mammals appeared among the earliest members of the group:

* Jaw joint - The dentary (the lower jaw bone, which carries the teeth) and the squamosal (a small cranial bone) meet to form the joint. In most gnathostomes, including early therapsids, the joint consists of the articular (a small bone at the back of the lower jaw) and quadrate (a small bone at the back of the upper jaw).
* Middle ear - In crown-group mammals, sound is carried from the eardrum by a chain of three bones, the malleus, the incus and the stapes. Ancestrally, the malleus and the incus are derived from the articular and the quadrate bones that constituted the jaw joint of early therapsids. 
* Tooth replacement - Teeth are replaced once or (as in toothed whales and murid rodents) not at all, rather than being replaced continually throughout life. 
* Prismatic enamel - The enamel coating on the surface of a tooth consists of prisms, solid, rod-like structures extending from the dentin to the tooth's surface. 
* Occipital condyles - Two knobs at the base of the skull fit into the topmost neck vertebra; most other tetrapods, in contrast, have only one such knob. 

For the most part, these characteristics were not present in the Triassic ancestors of the mammals.  Nearly all mammal groups possess an epipubic bone, the exception being modern placentals.

Biological systems

The majority of mammals have seven cervical vertebrae (bones in the neck), including bats, giraffes, whales and humans. The exceptions are the manatee and the two-toed sloth, which have just six, and the three-toed sloth which has nine cervical vertebrae.  All mammalian brains possess a neocortex, a brain region unique to mammals.  Placental mammals have a corpus callosum, unlike monotremes and marsupials. 

The lungs of mammals are spongy and honeycombed. Breathing is mainly achieved with the diaphragm, which divides the thorax from the abdominal cavity, forming a dome convex to the thorax. Contraction of the diaphragm flattens the dome, increasing the volume of the lung cavity. Air enters through the oral and nasal cavities, and travels through the larynx, trachea and bronchi, and expands the alveoli. Relaxing the diaphragm has the opposite effect, decreasing the volume of the lung cavity, causing air to be pushed out of the lungs. During exercise, the abdominal wall contracts, increasing pressure on the diaphragm, which forces air out quicker and more forcefully. The rib cage is able to expand and contract the chest cavity through the action of other respiratory muscles. Consequently, air is sucked into or expelled out of the lungs, always moving down its pressure gradient.  This type of lung is known as a bellows lung due to its resemblance to blacksmith bellows.

The integumentary system is made up of three layers: the outermost epidermis, the dermis and the hypodermis. The epidermis is typically 10 to 30 cells thick; its main function is to provide a waterproof layer. Its outermost cells are constantly lost; its bottommost cells are constantly dividing and pushing upward. The middle layer, the dermis, is 15 to 40 times thicker than the epidermis. The dermis is made up of many components, such as bony structures and blood vessels. The hypodermis is made up of adipose tissue. Its job is to store lipids, and to provide cushioning and insulation. The thickness of this layer varies widely from species to species. Although other animals have features such as whiskers, feathers, setae, or cilia that superficially resemble it, no animals other than mammals have hair. It is a definitive characteristic of the class. Though some mammals have very little, careful examination reveals the characteristic, often in obscure parts of their bodies.

Herbivores have developed a diverse range of physical structures to facilitate the consumption of plant material. To break up intact plant tissues, mammals have developed teeth structures that reflect their feeding preferences.  For instance, frugivores (animals that feed primarily on fruit) and herbivores that feed on soft foliage have low-crowned teeth specialized for grinding foliage and seeds. Grazing animals that tend to eat hard, silica-rich grasses, have high-crowned teeth, which are capable of grinding tough plant tissues and do not wear down as quickly as low-crowned teeth.   Most carnivorous mammals have carnassialiforme teeth (of varying length depending on diet), long canines and similar tooth replacement patterns.  

The stomach of Artiodactyls is divided into four sections: the rumen, the reticulum, the omasum and the abomasum (only ruminants have a rumen). After the plant material is consumed, it is mixed with saliva in the rumen and reticulum and separates into solid and liquid material. The solids lump together to form a bolus (or cud), and is regurgitated. When the bolus enters the mouth, the fluid is squeezed out with the tongue and swallowed again. Ingested food passes to the rumen and reticulum where cellulytic microbes (bacteria, protozoa and fungi) produce cellulase, which is needed to break down the cellulose in plants.  Perissodactyls, in contrast to the ruminants, store digested food that has left the stomach in an enlarged cecum, where it is fermented by bacteria.  Carnivora have a simple stomach adapted to digest primarily meat, as compared to the elaborate digestive systems of herbivorous animals, which are necessary to break down tough, complex plant fibers. The caecum is either absent or short and simple, and the large intestine is not sacculated or much wider than the small intestine. 

The mammalian heart has four chambers, two upper atria, the receiving chambers, and two lower ventricles, the discharging chambers.  The heart has four valves, which separate its chambers and ensures blood flows in the correct direction through the heart (preventing backflow). After gas exchange in the pulmonary capillaries (blood vessels in the lungs), oxygen-rich blood returns to the left atrium via one of the four pulmonary veins. Blood flows nearly continuously back into the atrium, which acts as the receiving chamber, and from here through an opening into the left ventricle. Most blood flows passively into the heart while both the atria and ventricles are relaxed, but toward the end of the ventricular relaxation period, the left atrium will contract, pumping blood into the ventricle. The heart also requires nutrients and oxygen found in blood like other muscles, and is supplied via coronary arteries. 

Color variation

Mammalian hair, also known as pelage, can vary in color between populations, organisms within a population, and even on the individual organism. Light-dark color variation is common in the mammalian taxa. Sometimes, this color variation is determined by age variation, however, in other cases, it is determined by other factors. Selective pressures, such as ecological interactions with other populations or environmental conditions, often lead to the variation in mammalian coloration.  These selective pressures favor certain colors in order to increase survival. Camouflage is thought to be a major selection pressure shaping coloration in mammals, although there is also evidence that sexual selection, communication and physiological processes may influence its evolution as well. 
Camouflage is the most predominant mechanism for color variation, as it aids in the concealment of the organisms from predators or from their prey. Sloths sometimes appear to have green fur and blend into their green jungle environment, but this color is caused by algal growths. 

Coat color can also be for intraspecies communication such as warning members of their species about predators, indicating health for reproductive purposes, communicating between mother and young and intimidating predators.
Studies have shown that in some cases, differences in female and male coat color could indicate information nutrition and hormone levels, which are important in the mate selection process. For example, some primates and marsupials have shades of violet, green, or blue skin on parts of their bodies, which indicates some distinct advantage in their largely arboreal habitat due to convergent evolution. 

Another mechanism for coat color variation is physiological response purposes, such as temperature regulation in tropical or arctic environments. Although much has been observed about color variation, much of the genetic that link coat color to genes is still unknown. The genetic sites where pigmentation genes are found are known to affect phenotype by altering the spatial distribution of pigmentation of the hairs, and altering the density and distribution of the hairs.  Although the genetic sites are known, it is largely unknown how these genes are expressed.

Reproductive system

Most mammals are viviparous, giving birth to live young. However, the five species of monotreme, the platypus and the four species of echidna, lay eggs. The monotremes have a sex determination system different from that of most other mammals.  In particular, the sex chromosomes of a platypus are more like those of a chicken than those of a therian mammal. 

The mammary glands of mammals are specialized to produce milk, the primary source of nutrition for newborns. The monotremes branched early from other mammals and do not have the nipples seen in most mammals, but they do have mammary glands. The young lick the milk from a mammary patch on the mother's belly. 

Viviparous mammals are in the subclass Theria; those living today are in the marsupial and placental infraclasses. Marsupials have a short gestation period, typically shorter than its estrous cycle and gives birth to an undeveloped newborn that then undergoes further development; in many species, this takes place within a pouch-like sac, the marsupium, located in the front of the mother's abdomen. This is the plesiomorphic condition among viviparous mammals; the presence of epipubic bones in all non-placental mammals prevents the expansion of the torso needed for full pregnancy. Even non-placental eutherians probably reproduced this way.  The placentals are unusual among mammals in giving birth to complete and fully developed young, usually after long gestation periods. 

Endothermy

Nearly all mammals are endothermic ("warm-blooded"). Most mammals also have hair to help keep them warm. Like birds, mammals can forage or hunt in weather and climates too cold for nonavian reptiles and large insects. Endothermy requires plenty of food energy, so mammals eat more food per unit of body weight than most reptiles.  Small insectivorous mammals eat prodigious amounts for their size. A rare exception, the naked mole-rat produces little metabolic heat, so it is considered an operational poikilotherm.  Birds are also endothermic, so endothermy is not unique to mammals. 

Behavior

Feeding

To maintain a high constant body temperature is energy expensive – mammals therefore need a nutritious and plentiful diet. While the earliest mammals were probably predators, different species have since adapted to meet their dietary requirements in a variety of ways. Some eat other animals – this is a carnivorous diet (and includes insectivorous diets). Other mammals, called herbivores, eat plants. An herbivorous diet includes subtypes such as granivory (seed eating), folivory (leaf eating), frugivory (fruit eating), nectivory (nectar eating), gummivory (gum eating) and mycophagy (fungus eating). Some mammals may be coprophagous, and consume feces, usually to consume more nutrients. An omnivore eats both prey and plants. Carnivorous mammals have a simple digestive tract because the proteins, lipids and minerals found in meat require little in the way of specialized digestion. Plants on the other hand contain complex carbohydrates, such as cellulose. The digestive tract of an herbivore is therefore host to bacteria that ferment these substances, and make them available for digestion. The bacteria are either housed in the multichambered stomach or in a large cecum. 

The size of an animal is also a factor in determining diet type (Allen's rule). Since small mammals have a high ratio of heat-losing surface area to heat-generating volume, they tend to have high energy requirements and a high metabolic rate. Mammals that weigh less than about 18 oz (500 g) are mostly insectivorous because they cannot tolerate the slow, complex digestive process of an herbivore. Larger animals, on the other hand, generate more heat and less of this heat is lost. They can therefore tolerate either a slower collection process (those that prey on larger vertebrates) or a slower digestive process (herbivores).  Furthermore, mammals that weigh more than 18 oz (500 g) usually cannot collect enough insects during their waking hours to sustain themselves. The only large insectivorous mammals are those that feed on huge colonies of insects (ants or termites).

Intelligence

In intelligent mammals, such as primates, the cerebrum is larger relative to the rest of the brain. Intelligence itself is not easy to define, but indications of intelligence include the ability to learn, matched with behavioral flexibility. Rats, for example, are considered to be highly intelligent, as they can learn and perform new tasks, an ability that may be important when they first colonize a fresh habitat. In some mammals, food gathering appears to be related to intelligence: a deer feeding on plants has a brain smaller than a cat, which must think to outwit its prey. 

Tool use by animals may indicate different levels of learning and cognition. The sea otter uses rocks as essential and regular parts of its foraging behaviour (smashing abalone off of rocks or breaking open shells), with some populations spending 21% of their time making tools.  Other tool use, such as chimpanzees using twigs to "fish" for termites, may be developed by watching others use tools and may even be a true example of animal teaching.  Tools may even be used in solving puzzles in which the animal appears to experience a "Eureka moment".  Other mammals that do not use tools, such as dogs, can also experience a Eureka moment. 

Brain size was previously considered a major indicator of the intelligence of an animal. Since most of the brain is used for maintaining bodily functions, greater ratios of brain to body mass may increase the amount of brain mass available for more complex cognitive tasks. Allometric analysis indicates that mammalian brain size scales at approximately the ⅔ or ¾ exponent of the body mass. Comparison of a particular animal's brain size with the expected brain size based on such allometric analysis provides an encephalisation quotient that can be used as another indication of animal intelligence.  Sperm whales have the largest brain mass of any animal on earth, averaging  and  in mature males. 

Self-awareness appears to be a sign of abstract thinking. Self-awareness, although not well-defined, is believed to be a precursor to more advanced processes such as metacognitive reasoning. The traditional method for measuring this is the mirror test, which determines if an animals possesses the ability of self-recognition.  Mammals that have 'passed' the mirror test are:
*Asian elephants, however not all subjects have passed. Three female elephants were tested, but only one passed, and two other elephants tested in another study also failed to pass. 
*Chimpanzees, but mirror tests with a juvenile (11 months old) male chimpanzee failed to reveal self-recognition.
*Bonobos  
*Bornean orangutan 
*Sumatran orangutan 
*Humans, which show signs of self-recognition at 18 months (mirror stage) 
*Bottlenose dolphins, since they don't have arms and can't touch the marked areas, decreased latency to approach the mirror, repetitious head circling and close viewing of the marked areas were considered signs of self-recognition  
*Killer whales  
*False killer whales 

Social structure

Eusociality is the highest level of social organization. These societies have an overlap of adult generations, the division of reproductive labor and cooperative caring of young. Usually insects, such as bees, ants and termites, have eusocial behavior, but it is demonstrated in two rodent species: the naked mole-rat  and the Damaraland mole-rat. 

Presociality is when animals exhibit more than just sexual interactions with members of the same species, but fall short of qualifying as eusocial. That is, presocial animals can display communal living, cooperative care of young, or primitive division of reproductive labor, but they do not display all of the three essential traits of eusocial animals. Humans and some species of Callitrichidae are unique among primates in their degree of cooperative care of young.  Harry Harlow set up an experiment with rhesus monkeys, presocial primates, in 1958; the results from this study showed that social encounters are necessary in order for the young monkeys to develop both mentally and sexually.Harlow, H.F. and Suomi, S.J. (1971). [http://www.pnas.org/cgi/content/abstract/68/7/1534 "Social Recovery by Isolation-Reared Monkeys"], Proceedings of the National Academy of Sciences of the United States of America, 68(7): 1534-1538

A fission-fusion society are societies that change frequently in their size and composition, making up a permanent social group called the "parent group". Permanent social networks consist of all individual members of a community and often varies to track changes in their environment. In a fission–fusion society, the main parent group can fracture (fission) into smaller stable subgroups or individuals to adapt to environmental or social circumstances. For example, a number of males may break off from the main group in order to hunt or forage for food during the day, but at night they may return to join (fusion) the primary group to share food and partake in other activities. Many mammals exhibit this, such as primates (for example orangutans and spider monkeys),  elephants,  hyenas,  lions,  and dolphins. 

Solitary animals defend a territory and avoid social interactions with the members of its species, except during breeding season. This is to avoid resource competition, as two individuals of the same species would occupy the same niche, and prevent depletion of food.  A solitary animal, while foraging, can also be less conspicuous to predators or prey. 

In a hierarchy, individuals are either dominant or submissive. A despotic hierarchy is where one individual is dominant while the others are submissive, as in wolves and lemurs,  and a pecking order which is a linear ranking of individuals where there is a top individual and a bottom individual. Pecking orders may also be ranked by sex, where the lowest individual of a sex has a higher ranking than the top individual of the other sex, as in hyenas.  Dominant individuals, or alphas, have a high chance of reproductive success, especially in harems where one or a few males (resident males) have exclusive breeding rights to females in a group.  Non-resident males can also be accepted in harems, but some species may be more strict. 

When two animals mate, they both share an interest in the success of the offspring, though often to different extremes. Unless the male and female are perfectly monogamous, meaning that they mate for life and take no other partners, even after the original mate’s death, as with wolves, Eurasian beavers, and otters. The amount of parental care will vary.   There are three types of polygamy: either one or multiple dominant males have with breeding rights (polygyny), multiple males that females mate with (polyandry), or multiple males have exclusive relations with multiple females (polygynandry). It is much more common for polygynous mating to happen, which, excluding leks, are estimated to occur in up to 90% of mammals.  Lek mating occurs in harems, wherein one or a few males protect their harem of females from other males who would otherwise mate with the females, as in elephant seals;  or males congregate around females and try to attract them with various courtship displays and vocalizations, as in harbor seals. 

Locomotion

Terrestrial

Most vertebrates—the amphibians, the reptiles and some mammals such as humans and bears—are plantigrade, walking on the whole of the underside of the foot.  Many mammals, such as cats and dogs are digitigrade, walking on their toes, the greater stride length allowing more speed. Digitigrade mammals are also often adept at quiet movement.  Some animals such as horses are unguligrade, walking on the tips of their toes. This even further increases their stride length and thus their speed.  A few mammals, namely the great apes, are also known to walk on their knuckles, at least for their front legs. Giant anteaters  and platypuses  are also knuckle-walkers.

Animals will use different gaits for different speeds, terrain and situations. For example, horses show four natural gaits, the slowest horse gait is the walk, then there are three faster gaits which, from slowest to fastest, are the trot, the canter and the gallop. Animals may also have unusual gaits that are used occasionally, such as for moving sideways or backwards. For example, the main human gaits are bipedal walking and running, but they employ many other gaits occasionally, including a four-legged crawl in tight spaces. Mammals show a vast range of gaits, the order that they place and lift their appendages in locomotion.  Gaits can be grouped into categories according to their patterns of support sequence.  For quadrupeds, there are three main categories: walking gaits, running gaits and leaping gaits.  Walking is the most common gait, where some feet are on the ground at any given time, and found in almost all legged animals. Running is considered to occur when at some points in the stride all feet are off the ground in a moment of suspension.

Arboreal

Arboreal animals frequently have elongated limbs that help them cross gaps, reach fruit or other resources, test the firmness of support ahead and, in some cases, to brachiate.Cartmill, M. (1985). Climbing. In Functional Vertebrate Morphology, eds. M. Hildebrand D. M. Bramble K. F. Liem and D. B. Wake), pp. 73–88. Cambridge: Belknap Press. Many arboreal species, such as tree porcupines, Silky Anteaters, spider monkeys and possums, use prehensile tails to grasp branches.  In the spider monkey, the tip of the tail has either a bare patch or adhesive pad, which provides increased friction. Claws can be used to interact with rough substrates and re-orient the direction of forces the animal applies.  This is what allows squirrels to climb tree trunks that are so large to be essentially flat from the perspective of such a small animal.  However, claws can interfere with an animal's ability to grasp very small branches, as they may wrap too far around and prick the animal's own paw. Frictional gripping is used by primates, relying upon hairless fingertips.  Squeezing the branch between the fingertips generates frictional force that holds the animal's hand to the branch.  However, this type of grip depends upon the angle of the frictional force, thus upon the diameter of the branch, with larger branches resulting in reduced gripping ability. To control descent, especially down large diameter branches, some arboreal animals such as squirrels have evolved highly mobile ankle joints that permit rotating the foot into a 'reversed' posture.  This allows the claws to hook into the rough surface of the bark, opposing the force of gravity. Small size provides many advantages to arboreal species: such as increasing the relative size of branches to the animal, lower center of mass, increased stability, lower mass (allowing movement on smaller branches) and the ability to move through more cluttered habitat. Size relating to weight affects gliding animals such as the sugar glider.  Some species of primate, bat and all species of sloth achieve passive stability by hanging beneath the branch. Both pitching and tipping become irrelevant, as the only method of failure would be losing their grip.

Aerial

Bats are the only mammals that can truly fly. They fly through the air at a constant speed by moving their wings up and down (usually with some fore-aft movement as well). Because the animal is in motion, there is some airflow relative to its body which, combined with the velocity of the wings, generates a faster airflow moving over the wing. This will generate a lift force vector pointing forwards and upwards, and a drag force vector pointing rearwards and upwards. The upwards components of these counteract gravity, keeping the body in the air, while the forward component provides thrust to counteract both the drag from the wing and from the body as a whole. 

The wings of bats are much thinner and consist of more bones than that of birds, allowing bats to maneuver more accurately and fly with more lift and less drag.  By folding the wings inwards towards their body on the upstroke, they use 35% less energy during flight than birds.  The membranes are delicate, ripping easily; however, the tissue of the bat's membrane is able to regrow, such that small tears can heal quickly.  The surface of their wings is equipped with touch-sensitive receptors on small bumps called Merkel cells, also found on human fingertips. These sensitive areas are different in bats, as each bump has a tiny hair in the center, making it even more sensitive and allowing the bat to detect and collect information about the air flowing over its wings, and to fly more efficiently by changing the shape of its wings in response. 

Fossorial

Fossorial creatures live in subterranean environments. Many fossorial mammals were classified under the, now obsolete, order Insectivora, such as shrews, hedgehogs and moles. Fossorial mammals have a fusiform body, thickest at the shoulders and tapering off at the tail and nose. Unable to see in the dark burrows, most have degenerated eyes, but degeneration varies between species; pocket gophers, for example, are only semi-fossorial and have very small yet functional eyes, in the fully fossorial marsupial mole the eyes are degenerated and useless, talpa moles have vestigial eyes and the cape golden mole has a layer of skin covering the eyes. External ears flaps are also very small or absent. Truly-fossorial mammals have short, stout legs as strength is more important than speed to a burrowing mammal, but semi-fossorial mammals have cursorial legs. The front paws are broad and have strong claws to help in loosening dirt while excavating burrows, and the back paws have webbing, as well as claws, which aids in throwing loosened dirt backwards. Most have large incisors to prevent dirt from flying into their mouth. 

Aquatic

Fully aquatic mammals, the cetaceans and sirenians, have lost their legs and have a tail fin to propel themselves through the water. Flipper movement is continuous. Whales swim by moving their tail fin and lower body up and down, propelling themselves through vertical movement, while their flippers are mainly used for steering. Their skeletal anatomy allows them to be fast swimmers. Most species have a dorsal fin to prevent themselves from turning upside-down in the water.   The flukes of sirenians are raised up and down in long strokes to move the animal forward, and can be twisted to turn. The forelimbs are paddle-like flippers which aid in turning and slowing. 

Semi-aquatic mammals, like pinnipeds, have two pairs of flippers on the front and back, the fore-flippers and hind-flippers. The elbows and ankles are enclosed within the body.Berta, pp. 62–64.  Pinnipeds have several adaptions for reducing drag. In addition to their streamlined bodies, they have smooth networks of muscle bundles in their skin that may increase laminar flow and make it easier for them to slip through water. They also lack arrector pili, so their fur can be streamlined as they swim. They rely on their fore-flippers for locomotion in a wing-like manner similar to penguins and sea turtles.  Fore-flipper movement is not continuous, and the animal glides between each stroke. Compared to terrestrial carnivorans, the fore-limbs are reduced in length, which gives the locomotor muscles at the shoulder and elbow joints greater mechanical advantage; the hind-flippers serve as stabilizers. Other semi-aquatic mammals include beavers, hippopotamuses, otters and platypuses.  Hippos are very large semi-aquatic mammals, and their barrel-shaped bodies have graviportal skeletal structures,  adapted to carrying their enormous weight, and their specific gravity allows them to sink and move along the bottom of a river. 

Hybrids

Hybrids are offspring resulting from the breeding of two genetically distinct individuals, which usually will result in a high degree of heterozygosity, though hybrid and heterozygous are not synonymous. The deliberate or accidental hybridizing of two or more species of closely related animals through captive breeding is a human activity which has been in existence for millennia and has grown for economic purposes (Domestication syndrome).  Hybrids between different subspecies within a species (such as between the Bengal tiger and Siberian tiger) are known as intra-specific hybrids. Hybrids between different species within the same genus (such as between lions and tigers) are known as interspecific hybrids or crosses. Hybrids between different genera (such as between sheep and goats) are known as intergeneric hybrids.  Natural hybrids will occur in hybrid zones, where two populations of species within the same genera or species living in the same or adjacent areas will interbreed with each other. Some hybrids have been recognized as species, such as the red wolf (though this is controversial). 

Artificial selection, the deliberate selective breeding of domestic animals, is being used to breed back recently extinct animals in an attempt to achieve an animal breed with a phenotype that resembles that extinct wildtype ancestor. A breeding-back (intraspecific) hybrid may be very similar to the extinct wild type in phenotype, ecological niche and to some extent genetics, but the initial gene pool of that wild type is lost forever with its extinction. As a result, some breeds, like Heck cattle, are vague look-alikes of the extinct wildtype aurochs. Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma. In certain organisms, these smaller substances are absorbed through the small intestine into the blood stream. Digestion is a form of catabolism that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term mechanical digestion refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. In chemical digestion, enzymes break down food into the small molecules the body can use.

In the human digestive system, food enters the mouth and mechanical digestion of the food starts by the action of mastication (chewing), a form of mechanical digestion, and the wetting contact of saliva. Saliva, a liquid secreted by the salivary glands, contains salivary amylase, an enzyme which starts the digestion of starch in the food; the saliva also contains mucus, which lubricates the food, and hydrogen carbonate, which provides the ideal conditions of pH (alkaline) for amylase to work. After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a bolus. It will then travel down the esophagus and into the stomach by the action of peristalsis. Gastric juice in the stomach starts protein digestion. Gastric juice mainly contains hydrochloric acid and pepsin. As these two chemicals may damage the stomach wall, mucus is secreted by the stomach, providing a slimy layer that acts as a shield against the damaging effects of the chemicals. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which is waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes.

After some time (typically 1–2 hours in humans, 4–6 hours in dogs, 3–4 hours in house cats), the resulting thick liquid is called chyme.  When the pyloric sphincter valve opens, chyme enters the duodenum where it mixes with digestive enzymes from the pancreas and bile juice from the liver and then passes through the small intestine, in which digestion continues. When the chyme is fully digested, it is absorbed into the blood. 95% of absorption of nutrients occurs in the small intestine.  Water and minerals are reabsorbed back into the blood in the colon (large intestine) where the pH is slightly acidic about 5.6 ~ 6.9.  Some vitamins, such as biotin and vitamin K (K2MK7) produced by bacteria in the colon are also absorbed into the blood in the colon. Waste material is eliminated from the rectum during defecation.

Digestive system

Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion developed earlier in evolutionary history, and most fungi still rely on it.  In this process, enzymes are secreted into the environment surrounding the organism, where they break down an organic material, and some of the products diffuse back to the organism. Animals have a tube (gastrointestinal tract) in which internal digestion occurs, which is more efficient because more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled. 

Some organisms, including nearly all spiders, simply secrete biotoxins and digestive chemicals (e.g., enzymes) into the extracellular environment prior to ingestion of the consequent "soup". In others, once potential nutrients or food is inside the organism, digestion can be conducted to a vesicle or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.

Secretion systems

Bacteria use several systems to obtain nutrients from other organisms in the environments.

Channel transport system

In a channel transupport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a simple system, which consists of only three protein subunits: the ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP). This secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 – 900 kDa). The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 900 kDa.

Molecular syringe

One molecular syringe is used through which a bacterium (e.g. certain types of Salmonella, Shigella, Yersinia) can inject nutrients into protist cells. One such mechanism was first discovered in Y. pestis and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than simply be secreted into the extracellular medium.Salyers, A. A. & Whitt, D. D. (2002). Bacterial Pathogenesis: A Molecular Approach, 2nd ed., Washington, D.C.: ASM Press. ISBN 1-55581-171-X

Conjugation machinery

The conjugation machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was discovered in Agrobacterium tumefaciens, which uses this system to introduce the Ti plasmid and proteins into the host, which develops the crown gall (tumor). The VirB complex of Agrobacterium tumefaciens is the prototypic system.

The nitrogen fixing Rhizobia are an interesting case, wherein conjugative elements naturally engage in inter-kingdom conjugation. Such elements as the Agrobacterium Ti or Ri plasmids contain elements that can transfer to plant cells. Transferred genes enter the plant cell nucleus and effectively transform the plant cells into factories for the production of opines, which the bacteria use as carbon and energy sources. Infected plant cells form crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant.

The Ti and Ri plasmids are themselves conjugative. Ti and Ri transfer between bacteria uses an independent system (the tra, or transfer, operon) from that for inter-kingdom transfer (the vir, or virulence, operon). Such transfer creates virulent strains from previously avirulent Agrobacteria.

Release of outer membrane vesicles

In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of outer membrane vesicles.   Portions of the outer membrane pinch off, forming spherical structures made of a lipid bilayer enclosing periplasmic materials.  Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells.  While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.

Gastrovascular cavity

The gastrovascular cavity functions as a stomach in both digestion and the distribution of nutrients to all parts of the body.  Extracellular digestion takes place within this central cavity, which is lined with the gastrodermis, the internal layer of epithelium. This cavity has only one opening to the outside that functions as both a mouth and an anus: waste and undigested matter is excreted through the mouth/anus, which can be described as an incomplete gut.

In a plant such as the Venus Flytrap that can make its own food through photosynthesis, it does not eat and digest its prey for the traditional objectives of harvesting energy and carbon, but mines prey primarily for essential nutrients (nitrogen and phosphorus in particular) that are in short supply in its boggy, acidic habitat.

Phagosome

A phagosome is a vacuole formed around a particle absorbed by phagocytosis.  The vacuole is formed by the fusion of the cell membrane around the particle. A phagosome is a cellular compartment in which pathogenic microorganisms can be killed and digested. Phagosomes fuse with lysosomes in their maturation process, forming phagolysosomes. In humans, Entamoeba histolytica can phagocytose red blood cells.

Specialised organs and behaviours

To aid in the digestion of their food animals evolved organs such as beaks, tongues, teeth, a crop, gizzard, and others.

Beaks

Birds have bony beaks that are specialised according to the bird's ecological niche. For example, macaws primarily eat seeds, nuts, and fruit, using their impressive beaks to open even the toughest seed. First they scratch a thin line with the sharp point of the beak, then they shear the seed open with the sides of the beak.

The mouth of the squid is equipped with a sharp horny beak mainly made of cross-linked proteins. It is used to kill and tear prey into manageable pieces. The beak is very robust, but does not contain any minerals, unlike the teeth and jaws of many other organisms, including marine species. The beak is the only indigestible part of the squid.

Tongue

The tongue is skeletal muscle on the floor of the mouth that manipulates food for chewing (mastication) and swallowing (deglutition). It is sensitive and kept moist by saliva. The underside of the tongue is covered with a smooth mucous membrane. The tongue also has a touch sense for locating and positioning food particles that require further chewing. The tongue is utilized to roll food particles into a bolus before being transported down the esophagus through peristalsis.

The sublingual region underneath the front of the tongue is a location where the oral mucosa is very thin, and underlain by a plexus of veins. This is an ideal location for introducing certain medications to the body. The sublingual route takes advantage of the highly vascular quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.

Teeth

Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.

The shapes, sizes and numbers of types of animals' teeth are related to their diets. For example, herbivores have a number of molars which are used to grind plant matter, which is difficult to digest. Carnivores have canine teeth which are used to kill and tear meat.

Crop

A crop, or croup, is a thin-walled expanded portion of the alimentary tract used for the storage of food prior to digestion. In some birds it is an expanded, muscular pouch near the gullet or throat. In adult doves and pigeons, the crop can produce crop milk to feed newly hatched birds.

Certain insects may have a crop or enlarged esophagus.

Abomasum

Herbivores have evolved cecums (or an abomasum in the case of ruminants). Ruminants have a fore-stomach with four chambers. These are the rumen, reticulum, omasum, and abomasum. In the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material.  Solids clump together to form the cud (or bolus). The cud is then regurgitated, chewed slowly to completely mix it with saliva and to break down the particle size.

Fibre, especially cellulose and hemi-cellulose, is primarily broken down into the volatile fatty acids, acetic acid, propionic acid and butyric acid in these chambers (the reticulo-rumen) by microbes: (bacteria, protozoa, and fungi). In the omasum, water and many of the inorganic mineral elements are absorbed into the blood stream.

The abomasum is the fourth and final stomach compartment in ruminants. It is a close equivalent of a monogastric stomach (e.g., those in humans or pigs), and digesta is processed here in much the same way. It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine.  Digesta is finally moved into the small intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulo-rumen are also digested in the small intestine.

Specialised behaviours

Regurgitation has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of pigeons and doves with which the parents feed their young by regurgitation. 

Many sharks have the ability to turn their stomachs inside out and evert it out of their mouths in order to get rid of unwanted contents (perhaps developed as a way to reduce exposure to toxins).

Other animals, such as rabbits and rodents, practise coprophagia behaviours – eating specialised faeces in order to re-digest food, especially in the case of roughage. Capybara, rabbits, hamsters and other related species do not have a complex digestive system as do, for example, ruminants. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft faecal pellets of partially digested food are excreted and generally consumed immediately. They also produce normal droppings, which are not eaten.

Young elephants, pandas, koalas, and hippos eat the faeces of their mother, probably to obtain the bacteria required to properly digest vegetation. When they are born, their intestines do not contain these bacteria (they are completely sterile). Without them, they would be unable to get any nutritional value from many plant components.

In earthworms

An earthworm's digestive system consists of a mouth, pharynx, esophagus, crop, gizzard, and intestine. The mouth is surrounded by strong lips, which act like a hand to grab pieces of dead grass, leaves, and weeds, with bits of soil to help chew. The lips break the food down into smaller pieces. In the pharynx, the food is lubricated by mucus secretions for easier passage. The esophagus adds calcium carbonate to neutralize the acids formed by food matter decay. Temporary storage occurs in the crop where food and calcium carbonate are mixed. The powerful muscles of the gizzard churn and mix the mass of food and dirt. When the churning is complete, the glands in the walls of the gizzard add enzymes to the thick paste, which helps chemically breakdown the organic matter. By peristalsis, the mixture is sent to the intestine where friendly bacteria continue chemical breakdown. This releases carbohydrates, protein, fat, and various vitamins and minerals for absorption into the body.

Overview of vertebrate digestion

In most vertebrates, digestion is a multistage process in the digestive system, starting from ingestion of raw materials, most often other organisms. Ingestion usually involves some type of mechanical and chemical processing. Digestion is separated into four steps:
# Ingestion: placing food into the mouth (entry of food in the digestive system),
# Mechanical and chemical breakdown:  mastication and the mixing of the resulting bolus with water, acids, bile and enzymes in the stomach and intestine to break down complex molecules into simple structures,
# Absorption: of nutrients from the digestive system to the circulatory and lymphatic capillaries through osmosis, active transport, and diffusion, and
# Egestion (Excretion): Removal of undigested materials from the digestive tract through defecation.

Underlying the process is muscle movement throughout the system through swallowing and peristalsis. Each step in digestion requires energy, and thus imposes an "overhead charge" on the energy made available from absorbed substances. Differences in that overhead cost are important influences on lifestyle, behavior, and even physical structures. Examples may be seen in humans, who differ considerably from other hominids (lack of hair, smaller jaws and musculature, different dentition, length of intestines, cooking, etc.).

The major part of digestion takes place in the small intestine. The large intestine primarily serves as a site for fermentation of indigestible matter by gut bacteria and for resorption of water from digests before excretion.

In mammals, preparation for digestion begins with the cephalic phase in which saliva is produced in the mouth and digestive enzymes are produced in the stomach.  Mechanical and chemical digestion begin in the mouth where food is chewed, and mixed with saliva to begin enzymatic processing of starches.  The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes. Absorption occurs in the stomach and gastrointestinal tract, and the process finishes with defecation.

Human digestion process

The human gastrointestinal tract is around 9 meters long. Food digestion physiology varies between individuals and upon other factors such as the characteristics of the food and size of the meal, and the process of digestion normally takes between 24 and 72 hours.

Different phases of digestion take place including: the cephalic phase , gastric phase, and intestinal phase. The cephalic phase occurs at the sight, thought and smell of food, which stimulate the cerebral cortex. Taste and smell stimuli are sent to the hypothalamus and medulla oblongata. After this it is routed through the vagus nerve and release of acetylcholine. Gastric secretion at this phase rises to 40% of maximum rate. Acidity in the stomach is not buffered by food at this point and thus acts to inhibit parietal (secretes acid) and G cell (secretes gastrin) activity via D cell secretion of somatostatin. The gastric phase takes 3 to 4 hours. It is stimulated by distension of the stomach, presence of food in stomach and decrease in pH. Distention activates long and myenteric reflexes. This activates the release of acetylcholine, which stimulates the release of more gastric juices. As protein enters the stomach, it binds to hydrogen ions, which raises the pH of the stomach. Inhibition of gastrin and gastric acid secretion is lifted. This triggers G cells to release gastrin, which in turn stimulates parietal cells to secrete gastric acid.  Gastric acid is about 0.5% hydrochloric acid (HCl), which lowers the pH to the desired pH of 1-3.  Acid release is also triggered by acetylcholine and histamine.
The intestinal phase has two parts, the excitatory and the inhibitory. Partially digested food fills the duodenum. This triggers intestinal gastrin to be released. Enterogastric reflex inhibits vagal nuclei, activating sympathetic fibers causing the pyloric sphincter to tighten to prevent more food from entering, and inhibits local reflexes.

Digestion begins in the mouth with the secretion of saliva and its digestive enzymes. Food is formed into a bolus by the mechanical mastication and swallowed into the esophagus from where it enters the stomach through the action of peristalsis. Gastric juice contains hydrochloric acid and pepsin which would damage the walls of the stomach and mucus is secreted for protection. In the stomach further release of enzymes break down the food further and this is combined with the churning action of the stomach. The partially digested food enters the duodenum as a thick semi-liquid chyme. In the small intestine, the larger part of digestion takes place and this is helped by the secretions of bile, pancreatic juice and intestinal juice.  The intestinal walls are lined with villi, and their epithelial cells is covered with numerous microvilli to improve the absorption of nutrients by increasing the surface area of the intestine.

In the large intestine the passage of food is slower to enable fermentation by the gut flora to take place. Here water is absorbed and waste material stored as feces to be removed by defecation via the anal canal and anus.

Breakdown into nutrients

Protein digestion

Protein digestion occurs in the stomach and duodenum in which 3 main enzymes, pepsin secreted by the stomach and trypsin and chymotrypsin secreted by the pancreas, break down food proteins into polypeptides that are then broken down by various exopeptidases and dipeptidases into amino acids.  The digestive enzymes however are mostly secreted as their inactive precursors, the zymogens.  For example, trypsin is secreted by pancreas in the form of trypsinogen, which is activated in the duodenum by enterokinase to form trypsin.  Trypsin then cleaves proteins to smaller polypeptides.

Fat digestion
 

Digestion of some fats can begin in the mouth where lingual lipase breaks down some short chain lipids into diglycerides. However fats are mainly digested in the small intestine.   The presence of fat in the small intestine produces hormones that stimulate the release of pancreatic lipase from the pancreas and bile from the liver which helps in the emulsification of fats for absorption of fatty acids.  Complete digestion of one molecule of fat (a triglyceride) results a mixture of  fatty acids, mono- and di-glycerides, as well as some undigested triglycerides, but no free glycerol molecules.

Carbohydrate digestion

In humans, dietary starches are composed of glucose units arranged in long chains called amylose, a polysaccharide. During digestion, bonds between glucose molecules are broken by salivary and pancreatic amylase, resulting in progressively smaller chains of glucose.  This results in simple sugars glucose and maltose (2 glucose molecules) that can be absorbed by the small intestine.

Lactase is an enzyme that breaks down the disaccharide lactose to its component parts, glucose and galactose.  Glucose and galactose can be absorbed by the small intestine.  Approximately 65 percent of the adult population produce only small amounts of lactase and are unable to eat unfermented milk-based foods.  This is commonly known as lactose intolerance.  Lactose intolerance varies widely by ethnic heritage;  more than 90 percent of peoples of east Asian descent are lactose intolerant, in contrast to about 5 percent of people of northern European descent. 

Sucrase is an enzyme that breaks down the disaccharide sucrose, commonly known as table sugar, cane sugar, or beet sugar. Sucrose digestion yields the sugars fructose and glucose which are readily absorbed by the small intestine.

DNA and RNA digestion

DNA and RNA are broken down into mononucleotides by the nucleases deoxyribonuclease and ribonuclease (DNase and RNase) from the pancreas.

Non-destructive digestion

Some nutrients are complex molecules (for example vitamin B12) which would be destroyed if they were broken down into their functional groups.  To digest vitamin B12 non-destructively, haptocorrin in saliva strongly binds and protects the B12 molecules from stomach acid as they enter the stomach and are cleaved from their protein complexes. 

After the B12-haptocorrin complexes pass from the stomach via the pylorus to the duodenum, pancreatic proteases cleave haptocorrin from the B12 molecules which rebind to intrinsic factor (IF).  These B12-IF complexes travel to the ileum portion of the small intestine where cubilin receptors enable assimilation and circulation of B12-IF complexes in the blood. 

Digestive hormones

There are at least five hormones that aid and regulate the digestive system in mammals. There are variations across the vertebrates, as for instance in birds. Arrangements are complex and additional details are regularly discovered. For instance, more connections to metabolic control (largely the glucose-insulin system) have been uncovered in recent years.

* Gastrin – is in the stomach and stimulates the gastric glands to secrete pepsinogen (an inactive form of the enzyme pepsin) and hydrochloric acid. Secretion of gastrin is stimulated by food arriving in stomach. The secretion is inhibited by low pH.
* Secretin – is in the duodenum and signals the secretion of sodium bicarbonate in the pancreas and it stimulates the bile secretion in the liver.  This hormone responds to the acidity of the chyme.
* Cholecystokinin (CCK) – is in the duodenum and stimulates the release of digestive enzymes in the pancreas and stimulates the emptying of bile in the gall bladder. This hormone is secreted in response to fat in chyme.
* Gastric inhibitory peptide (GIP) – is in the duodenum and decreases the stomach churning in turn slowing the emptying in the stomach. Another function is to induce insulin secretion.
* Motilin – is in the duodenum and increases the migrating myoelectric complex component of gastrointestinal motility and stimulates the production of pepsin.

Significance of pH

Digestion is a complex process controlled by several factors. pH plays a crucial role in a normally functioning digestive tract. In the mouth, pharynx and esophagus, pH is typically about 6.8, very weakly acidic. Saliva controls pH in this region of the digestive tract. Salivary amylase is contained in saliva and starts the breakdown of carbohydrates into monosaccharides. Most digestive enzymes are sensitive to pH and will denature in a high or low pH environment.

The stomach's high acidity inhibits the breakdown of carbohydrates within it. This acidity confers two benefits: it denatures proteins for further digestion in the small intestines, and provides non-specific immunity, damaging or eliminating various pathogens.

In the small intestines, the duodenum provides critical pH balancing to activate digestive enzymes. The liver secretes bile into the duodenum to neutralize the acidic conditions from the stomach, and the pancreatic duct empties into the duodenum, adding bicarbonate to neutralize the acidic chyme, thus creating a neutral environment. The mucosal tissue of the small intestines is alkaline with a pH of about 8.5.
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