In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. While these definitions may seem adequate, when looked at more they represent problematic species concepts. For example, the boundaries between related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, in a ring species. Among organisms that reproduce only asexually, the concept of a reproductive species breaks down, each clone is a microspecies. All species are given a two-part name, a "binomial"; the first part of a binomial is the genus.
The second part is called the specific epithet. For example, Boa constrictor is one of four species of the genus Boa. None of these is satisfactory definitions, but scientists and conservationists need a species definition which allows them to work, regardless of the theoretical difficulties. If species were fixed and distinct from one another, there would be no problem, but evolutionary processes cause species to change continually, to grade into one another. Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped. Charles Darwin's 1859 book The Origin of Species explained how species could arise by natural selection; that understanding was extended in the 20th century through genetics and population ecology. Genetic variability arises from mutations and recombination, while organisms themselves are mobile, leading to geographical isolation and genetic drift with varying selection pressures.
Genes can sometimes be exchanged between species by horizontal gene transfer. Viruses are a special case, driven by a balance of mutation and selection, can be treated as quasispecies. Biologists and taxonomists have made many attempts to define species, beginning from morphology and moving towards genetics. Early taxonomists such as Linnaeus had no option but to describe what they saw: this was formalised as the typological or morphological species concept. Ernst Mayr emphasised reproductive isolation, but this, like other species concepts, is hard or impossible to test. Biologists have tried to refine Mayr's definition with the recognition and cohesion concepts, among others. Many of the concepts are quite similar or overlap, so they are not easy to count: the biologist R. L. Mayden recorded about 24 concepts, the philosopher of science John Wilkins counted 26. Wilkins further grouped the species concepts into seven basic kinds of concepts: agamospecies for asexual organisms biospecies for reproductively isolated sexual organisms ecospecies based on ecological niches evolutionary species based on lineage genetic species based on gene pool morphospecies based on form or phenotype and taxonomic species, a species as determined by a taxonomist.
A typological species is a group of organisms in which individuals conform to certain fixed properties, so that pre-literate people recognise the same taxon as do modern taxonomists. The clusters of variations or phenotypes within specimens would differentiate the species; this method was used as a "classical" method of determining species, such as with Linnaeus early in evolutionary theory. However, different phenotypes are not different species. Species named in this manner are called morphospecies. In the 1970s, Robert R. Sokal, Theodore J. Crovello and Peter Sneath proposed a variation on this, a phenetic species, defined as a set of organisms with a similar phenotype to each other, but a different phenotype from other sets of organisms, it differs from the morphological species concept in including a numerical measure of distance or similarity to cluster entities based on multivariate comparisons of a reasonably large number of phenotypic traits. A mate-recognition species is a group of sexually reproducing organisms that recognize one another as potential mates.
Expanding on this to allow for post-mating isolation, a cohesion species is the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. A further development of the recognition concept is provided by the biosemiotic concept of species. In microbiology, genes can move even between distantly related bacteria extending to the whole bacterial domain; as a rule of thumb, microbiologists have assumed that kinds of Bacteria or Archaea with 16S ribosomal RNA gene sequences more similar than 97% to each other need to be checked by DNA-DNA hybridisation to decide if they belong to the same species or not. This concept was narrowed in 2006 to a similarity of 98.7%. DNA-DNA hybri
A fossil is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, exoskeletons, stone imprints of animals or microbes, objects preserved in amber, petrified wood, coal, DNA remnants; the totality of fossils is known as the fossil record. Paleontology is the study of fossils: their age, method of formation, evolutionary significance. Specimens are considered to be fossils if they are over 10,000 years old; the oldest fossils are around 3.48 billion years old to 4.1 billion years old. The observation in the 19th century that certain fossils were associated with certain rock strata led to the recognition of a geological timescale and the relative ages of different fossils; the development of radiometric dating techniques in the early 20th century allowed scientists to quantitatively measure the absolute ages of rocks and the fossils they host. There are many processes that lead to fossilization, including permineralization and molds, authigenic mineralization and recrystallization, adpression and bioimmuration.
Fossils vary in size from one-micrometre bacteria to dinosaurs and trees, many meters long and weighing many tons. A fossil preserves only a portion of the deceased organism that portion, mineralized during life, such as the bones and teeth of vertebrates, or the chitinous or calcareous exoskeletons of invertebrates. Fossils may consist of the marks left behind by the organism while it was alive, such as animal tracks or feces; these types of fossil are called trace ichnofossils, as opposed to body fossils. Some fossils are called chemofossils or biosignatures; the process of fossilization varies according to external conditions. Permineralization is a process of fossilization; the empty spaces within an organism become filled with mineral-rich groundwater. Minerals precipitate from the groundwater; this process can occur in small spaces, such as within the cell wall of a plant cell. Small scale permineralization can produce detailed fossils. For permineralization to occur, the organism must become covered by sediment soon after death, otherwise decay commences.
The degree to which the remains are decayed when covered determines the details of the fossil. Some fossils consist only of skeletal teeth; this is a form of diagenesis. In some cases, the original remains of the organism dissolve or are otherwise destroyed; the remaining organism-shaped hole in the rock is called an external mold. If this hole is filled with other minerals, it is a cast. An endocast, or internal mold, is formed when sediments or minerals fill the internal cavity of an organism, such as the inside of a bivalve or snail or the hollow of a skull; this is a special form of mold formation. If the chemistry is right, the organism can act as a nucleus for the precipitation of minerals such as siderite, resulting in a nodule forming around it. If this happens before significant decay to the organic tissue fine three-dimensional morphological detail can be preserved. Nodules from the Carboniferous Mazon Creek fossil beds of Illinois, USA, are among the best documented examples of such mineralization.
Replacement occurs. In some cases mineral replacement of the original shell occurs so and at such fine scales that microstructural features are preserved despite the total loss of original material. A shell is said to be recrystallized when the original skeletal compounds are still present but in a different crystal form, as from aragonite to calcite. Compression fossils, such as those of fossil ferns, are the result of chemical reduction of the complex organic molecules composing the organism's tissues. In this case the fossil consists of original material, albeit in a geochemically altered state; this chemical change is an expression of diagenesis. What remains is a carbonaceous film known as a phytoleim, in which case the fossil is known as a compression. However, the phytoleim is lost and all that remains is an impression of the organism in the rock—an impression fossil. In many cases, however and impressions occur together. For instance, when the rock is broken open, the phytoleim will be attached to one part, whereas the counterpart will just be an impression.
For this reason, one term covers the two modes of preservation: adpression. Because of their antiquity, an unexpected exception to the alteration of an organism's tissues by chemical reduction of the complex organic molecules during fossilization has been the discovery of soft tissue in dinosaur fossils, including blood vessels, the isolation of proteins and evidence for DNA fragments. In 2014, Mary Schweitzer and her colleagues reported the presence of iron particles associated with soft tissues recovered from dinosaur fossils. Based on various experiments that studied the interaction of iron in haemoglobin with blood vessel tissue they proposed that solution hypoxia coupled with iron chelation enhances the stability and preservation of soft tissue and provides the basis for an explanation for the unforeseen preservation of fossil soft tissues. However, a older study based on eight taxa ranging in time from the Devonian to the Jurassic found that reasonably well-preserved fibrils that represent collagen were preser
Punctuated equilibrium is a theory in evolutionary biology which proposes that once species appear in the fossil record the population will become stable, showing little evolutionary change for most of its geological history. This state of little or no morphological change is called stasis; when significant evolutionary change occurs, the theory proposes that it is restricted to rare and geologically rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which a species splits into two distinct species, rather than one species transforming into another. Punctuated equilibrium is contrasted against phyletic gradualism, the idea that evolution occurs uniformly and by the steady and gradual transformation of whole lineages. In this view, evolution is seen as smooth and continuous. In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing their theory and called it punctuated equilibria, their paper built upon Ernst Mayr's model of geographic speciation, I.
Michael Lerner's theories of developmental and genetic homeostasis, their own empirical research. Eldredge and Gould proposed that the degree of gradualism attributed to Charles Darwin is nonexistent in the fossil record, that stasis dominates the history of most fossil species. Punctuated equilibrium originated as a logical consequence of Ernst Mayr's concept of genetic revolutions by allopatric and peripatric speciation as applied to the fossil record. Although the sudden appearance of species and its relationship to speciation was proposed and identified by Mayr in 1954, historians of science recognize the 1972 Eldredge and Gould paper as the basis of the new paleobiological research program. Punctuated equilibrium differs from Mayr's ideas in that Eldredge and Gould placed greater emphasis on stasis, whereas Mayr was concerned with explaining the morphological discontinuity found in the fossil record. Mayr complimented Eldredge and Gould's paper, stating that evolutionary stasis had been "unexpected by most evolutionary biologists" and that punctuated equilibrium "had a major impact on paleontology and evolutionary biology."A year before their 1972 Eldredge and Gould paper, Niles Eldredge published a paper in the journal Evolution which suggested that gradual evolution was seen in the fossil record and argued that Ernst Mayr's standard mechanism of allopatric speciation might suggest a possible resolution.
The Eldredge and Gould paper was presented at the Annual Meeting of the Geological Society of America in 1971. The symposium focused its attention on how modern microevolutionary studies could revitalize various aspects of paleontology and macroevolution. Tom Schopf, who organized that year's meeting, assigned Gould the topic of speciation. Gould recalls that "Eldredge's 1971 publication had presented the only new and interesting ideas on the paleontological implications of the subject—so I asked Schopf if we could present the paper jointly." According to Gould "the ideas came from Niles, with yours acting as a sounding board and eventual scribe. I coined the term punctuated equilibrium and wrote most of our 1972 paper, but Niles is the proper first author in our pairing of Eldredge and Gould." In his book Time Frames Eldredge recalls that after much discussion the pair "each wrote half. Some of the parts that would seem the work of one of us were first penned by the other—I remember for example, writing the section on Gould's snails.
Other parts are harder to reconstruct. Gould edited the entire manuscript for better consistency. We sent it in, Schopf reacted against it—thus signaling the tenor of the reaction it has engendered, though for shifting reasons, down to the present day."John Wilkins and Gareth Nelson have argued that French architect Pierre Trémaux proposed an "anticipation of the theory of punctuated equilibrium of Gould and Eldredge." The fossil record includes well documented examples of both phyletic gradualism and punctuational evolution. As such, much debate persists over the prominence of stasis in the fossil record. Before punctuated equilibrium, most evolutionists considered stasis to be unimportant; the paleontologist George Gaylord Simpson, for example, believed that phyletic gradual evolution comprised 90% of evolution. More modern studies, including a meta-analysis examining 58 published studies on speciation patterns in the fossil record showed that 71% of species exhibited stasis, 63% were associated with punctuated patterns of evolutionary change.
According to Michael Benton, "it seems clear that stasis is common, that had not been predicted from modern genetic studies." A paramount example of evolutionary stasis is the fern Osmunda claytoniana. Based on paleontological evidence it has remained unchanged at the level of fossilized nuclei and chromosomes, for at least 180 million years; when Eldredge and Gould published their 1972 paper, allopatric speciation was considered the "standard" model of speciation. This model was popularized by Ernst Mayr in his 1954 paper "Change of genetic environment and evolution," and his classic volume Animal Species and Evolution. Allopatric speciation suggests that species with large central populations are stabilized by their large volume and the process of gene flow. New and beneficial mutations are diluted by the population's large size and are unable to reach fixation, due to such factors as changing environments. If this is the case the transformation of whole lineages should be rare, as the fossil record indicates.
An extinction event is a widespread and rapid decrease in the biodiversity on Earth. Such an event is identified by a sharp change in the diversity and abundance of multicellular organisms, it occurs. Estimates of the number of major mass extinctions in the last 540 million years range from as few as five to more than twenty; these differences stem from the threshold chosen for describing an extinction event as "major", the data chosen to measure past diversity. Because most diversity and biomass on Earth is microbial, thus difficult to measure, recorded extinction events affect the observed, biologically complex component of the biosphere rather than the total diversity and abundance of life. Extinction occurs at an uneven rate. Based on the fossil record, the background rate of extinctions on Earth is about two to five taxonomic families of marine animals every million years. Marine fossils are used to measure extinction rates because of their superior fossil record and stratigraphic range compared to land animals.
The Great Oxygenation Event, which occurred around 2.45 billion years ago, was the first major extinction event. Since the Cambrian explosion five further major mass extinctions have exceeded the background extinction rate; the most recent and arguably best-known, the Cretaceous–Paleogene extinction event, which occurred 66 million years ago, was a large-scale mass extinction of animal and plant species in a geologically short period of time. In addition to the five major mass extinctions, there are numerous minor ones as well, the ongoing mass extinction caused by human activity is sometimes called the sixth extinction. Mass extinctions seem to be a Phanerozoic phenomenon, with extinction rates low before large complex organisms arose. In a landmark paper published in 1982, Jack Sepkoski and David M. Raup identified five mass extinctions, they were identified as outliers to a general trend of decreasing extinction rates during the Phanerozoic, but as more stringent statistical tests have been applied to the accumulating data, it has been established that multicellular animal life has experienced five major and many minor mass extinctions.
The "Big Five" cannot be so defined, but rather appear to represent the largest of a smooth continuum of extinction events. Ordovician–Silurian extinction events: 450–440 Ma at the Ordovician–Silurian transition. Two events occurred that killed off 27% of all families, 57% of all genera and 60% to 70% of all species. Together they are ranked by many scientists as the second largest of the five major extinctions in Earth's history in terms of percentage of genera that became extinct. Late Devonian extinction: 375–360 Ma near the Devonian–Carboniferous transition. At the end of the Frasnian Age in the part of the Devonian Period, a prolonged series of extinctions eliminated about 19% of all families, 50% of all genera and at least 70% of all species; this extinction event lasted as long as 20 million years, there is evidence for a series of extinction pulses within this period. Permian–Triassic extinction event: 252 Ma at the Permian–Triassic transition. Earth's largest extinction killed 57% of all families, 83% of all genera and 90% to 96% of all species.
The successful marine arthropod, the trilobite, became extinct. The evidence regarding plants is less clear; the "Great Dying" had enormous evolutionary significance: on land, it ended the primacy of mammal-like reptiles. The recovery of vertebrates took 30 million years, but the vacant niches created the opportunity for archosaurs to become ascendant. In the seas, the percentage of animals that were sessile dropped from 67% to 50%; the whole late Permian was a difficult time for at least marine life before the "Great Dying". Triassic–Jurassic extinction event: 201.3 Ma at the Triassic–Jurassic transition. About 23% of all families, 48% of all genera and 70% to 75% of all species became extinct. Most non-dinosaurian archosaurs, most therapsids, most of the large amphibians were eliminated, leaving dinosaurs with little terrestrial competition. Non-dinosaurian archosaurs continued to dominate aquatic environments, while non-archosaurian diapsids continued to dominate marine environments; the Temnospondyl lineage of large amphibians survived until the Cretaceous in Australia.
Cretaceous–Paleogene extinction event: 66 Ma at the Cretaceous – Paleogene transition interval. The event called the Cretaceous-Tertiary or K–T extinction or K–T boundary is now named the Cretaceous–Paleogene extinction event. About 17% of all families, 50% of all genera and 75% of all species became extinct. In the seas all the ammonites and mosasaurs disappeared and the percentage of sessile animals was reduced to about 33%. All non-avian dinosaurs became extinct during that time; the boundary event was severe with a significant amount of variability in the rate of extinction between and among different clades. Mammals and birds, the latter descended from theropod dinosaurs, emerged as dominant large land animals. Despite the popularization of these five events, there is no definite line separating them from other extinction events.